Starting phenix.real_space_refine on Tue Feb 20 17:58:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we8_32442/02_2024/7we8_32442.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we8_32442/02_2024/7we8_32442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we8_32442/02_2024/7we8_32442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we8_32442/02_2024/7we8_32442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we8_32442/02_2024/7we8_32442.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we8_32442/02_2024/7we8_32442.pdb" } resolution = 3.5 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= 0.000 sd= 0.002 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 123 5.16 5 C 18217 2.51 5 N 4668 2.21 5 O 5577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 149": "OE1" <-> "OE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 742": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28585 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 800 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 15.20, per 1000 atoms: 0.53 Number of scatterers: 28585 At special positions: 0 Unit cell: (147.66, 144.45, 236.47, 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 123 16.00 O 5577 8.00 N 4668 7.00 C 18217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 134 " distance=2.02 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.04 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " 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=3, 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A1301 " - " ASN A1155 " " NAG A1302 " - " ASN A 143 " " NAG A1303 " - " ASN A 17 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 600 " " NAG A1306 " - " ASN A 654 " " NAG A1307 " - " ASN A 613 " " NAG A1308 " - " ASN A 706 " " NAG B1301 " - " ASN B1155 " " NAG B1302 " - " ASN B 123 " " NAG B1303 " - " ASN B 143 " " NAG B1304 " - " ASN B 17 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 600 " " NAG B1307 " - " ASN B 654 " " NAG B1308 " - " ASN B 613 " " NAG B1309 " - " ASN B 706 " " NAG C1301 " - " ASN C1155 " " NAG C1302 " - " ASN C 123 " " NAG C1303 " - " ASN C 143 " " NAG C1304 " - " ASN C 17 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 600 " " NAG C1307 " - " ASN C 654 " " NAG C1308 " - " ASN C 613 " " NAG C1309 " - " ASN C 706 " " NAG D 1 " - " ASN A 231 " " NAG F 1 " - " ASN A 714 " " NAG G 1 " - " ASN A1071 " " NAG I 1 " - " ASN A 798 " " NAG J 1 " - " ASN A1095 " " NAG K 1 " - " ASN A1131 " " NAG M 1 " - " ASN B 714 " " NAG O 1 " - " ASN B 798 " " NAG P 1 " - " ASN B1095 " " NAG Q 1 " - " ASN B1131 " " NAG R 1 " - " ASN B 328 " " NAG T 1 " - " ASN C 714 " " NAG V 1 " - " ASN C 798 " " NAG W 1 " - " ASN C1095 " " NAG X 1 " - " ASN C1131 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.89 Conformation dependent library (CDL) restraints added in 5.3 seconds 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6612 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 57 sheets defined 24.0% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.528A pdb=" N LEU A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.931A pdb=" N LEU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 402 through 408 removed outlier: 5.157A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 734 through 741 removed outlier: 3.524A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 751 removed outlier: 3.575A pdb=" N LEU A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 756 through 780 removed outlier: 3.639A pdb=" N LYS A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A 762 " --> pdb=" O THR A 758 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 removed outlier: 3.586A pdb=" N LEU A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 819 " --> pdb=" O ILE A 815 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.507A pdb=" N GLN A 850 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS A 851 " --> pdb=" O CYS A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 881 removed outlier: 3.523A pdb=" N ALA A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 870 " --> pdb=" O MET A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.678A pdb=" N ALA A 887 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 907 removed outlier: 4.406A pdb=" N ALA A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.933A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.838A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 936 " --> pdb=" O GLN A 932 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR A 938 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 963 removed outlier: 4.064A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 952 " --> pdb=" O VAL A 948 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 955 " --> pdb=" O HIS A 951 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 980 removed outlier: 4.076A pdb=" N SER A 979 " --> pdb=" O ASN A 975 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 975 through 980' Processing helix chain 'A' and resid 985 through 1030 removed outlier: 3.659A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 998 " --> pdb=" O ILE A 994 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A1017 " --> pdb=" O ALA A1013 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1030 " --> pdb=" O MET A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1115 No H-bonds generated for 'chain 'A' and resid 1113 through 1115' Processing helix chain 'A' and resid 1137 through 1157 removed outlier: 3.875A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS A1151 " --> pdb=" O GLU A1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 361 through 368 removed outlier: 4.166A pdb=" N LEU B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 386 removed outlier: 4.169A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP B 386 " --> pdb=" O LYS B 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 382 through 386' Processing helix chain 'B' and resid 402 through 408 removed outlier: 5.150A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 406 " --> pdb=" O GLU B 403 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 408 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.870A pdb=" N SER B 634 " --> pdb=" O TRP B 630 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 635 " --> pdb=" O ARG B 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 630 through 635' Processing helix chain 'B' and resid 734 through 740 removed outlier: 3.620A pdb=" N TYR B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 751 removed outlier: 3.572A pdb=" N LEU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.550A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.886A pdb=" N LEU B 818 " --> pdb=" O PHE B 814 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 819 " --> pdb=" O ILE B 815 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 removed outlier: 3.557A pdb=" N TYR B 870 " --> pdb=" O MET B 866 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 879 " --> pdb=" O LEU B 875 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 894 through 907 removed outlier: 3.879A pdb=" N ALA B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 removed outlier: 4.046A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 928 removed outlier: 3.553A pdb=" N ILE B 928 " --> pdb=" O PHE B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 938 removed outlier: 3.777A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 936 " --> pdb=" O GLN B 932 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR B 938 " --> pdb=" O SER B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 942 through 963 removed outlier: 4.194A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 980 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.006A pdb=" N GLU B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY B 996 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B1030 " --> pdb=" O MET B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1115 No H-bonds generated for 'chain 'B' and resid 1113 through 1115' Processing helix chain 'B' and resid 1138 through 1155 removed outlier: 4.124A pdb=" N GLU B1147 " --> pdb=" O ASP B1143 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B1148 " --> pdb=" O SER B1144 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B1155 " --> pdb=" O LYS B1151 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.879A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP C 386 " --> pdb=" O LYS C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 408 removed outlier: 3.542A pdb=" N GLU C 403 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 404 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C 408 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.550A pdb=" N ASN C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.846A pdb=" N TYR C 633 " --> pdb=" O TRP C 630 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR C 635 " --> pdb=" O VAL C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 removed outlier: 3.613A pdb=" N TYR C 738 " --> pdb=" O ASP C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 752 removed outlier: 3.774A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU C 749 " --> pdb=" O GLU C 745 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 754 No H-bonds generated for 'chain 'C' and resid 753 through 754' Processing helix chain 'C' and resid 755 through 756 No H-bonds generated for 'chain 'C' and resid 755 through 756' Processing helix chain 'C' and resid 757 through 775 removed outlier: 3.664A pdb=" N LYS C 761 " --> pdb=" O CYS C 757 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 767 " --> pdb=" O ALA C 763 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 removed outlier: 3.503A pdb=" N PHE C 779 " --> pdb=" O THR C 775 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C 780 " --> pdb=" O GLN C 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 775 through 780' Processing helix chain 'C' and resid 813 through 822 removed outlier: 3.607A pdb=" N LEU C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 820 " --> pdb=" O GLU C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 853 Processing helix chain 'C' and resid 863 through 881 removed outlier: 3.565A pdb=" N ILE C 867 " --> pdb=" O THR C 863 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN C 869 " --> pdb=" O GLU C 865 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER C 881 " --> pdb=" O GLY C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 907 removed outlier: 3.516A pdb=" N MET C 899 " --> pdb=" O PHE C 895 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 902 " --> pdb=" O GLN C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.981A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 916 " --> pdb=" O VAL C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 removed outlier: 3.559A pdb=" N GLY C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 931 " --> pdb=" O ALA C 927 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER C 936 " --> pdb=" O GLN C 932 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR C 938 " --> pdb=" O SER C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 963 removed outlier: 4.606A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU C 956 " --> pdb=" O ASN C 952 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN C 957 " --> pdb=" O ALA C 953 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 979 removed outlier: 4.313A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C 978 " --> pdb=" O LEU C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.187A pdb=" N GLU C 987 " --> pdb=" O LYS C 983 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL C 988 " --> pdb=" O VAL C 984 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY C 996 " --> pdb=" O ARG C 992 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR C1004 " --> pdb=" O SER C1000 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C1017 " --> pdb=" O ALA C1013 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU C1021 " --> pdb=" O ALA C1017 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C1030 " --> pdb=" O MET C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1115 No H-bonds generated for 'chain 'C' and resid 1113 through 1115' Processing helix chain 'C' and resid 1138 through 1143 Processing helix chain 'C' and resid 1145 through 1158 Processing helix chain 'L' and resid 26 through 31 Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.966A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.858A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 261 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.979A pdb=" N PHE A 43 " --> pdb=" O ARG B 564 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.916A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.259A pdb=" N PHE A 163 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.861A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 646 " --> pdb=" O TYR A 609 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY A 645 " --> pdb=" O THR A 642 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.648A pdb=" N TYR A 393 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 511 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 430 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS A 375 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 432 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.828A pdb=" N TYR A 470 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.848A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 548 through 551 removed outlier: 3.517A pdb=" N THR A 585 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 562 through 563 removed outlier: 3.520A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.803A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 692 " --> pdb=" O CYS A 668 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 668 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 709 through 712 removed outlier: 3.588A pdb=" N ILE A 711 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A1070 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.665A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 732 through 733 Processing sheet with id=AB8, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AB9, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 6.011A pdb=" N VAL A1119 " --> pdb=" O PHE A1086 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE A1086 " --> pdb=" O VAL A1119 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLY A1121 " --> pdb=" O ALA A1084 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.859A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA B 261 " --> pdb=" O ILE B 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.004A pdb=" N VAL B 36 " --> pdb=" O LEU B 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.187A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 163 through 167 removed outlier: 3.914A pdb=" N VAL B 125 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 118 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 115 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE B 117 " --> pdb=" O TRP B 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 308 through 311 removed outlier: 3.557A pdb=" N THR B 596 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 640 " --> pdb=" O LEU B 647 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 315 through 316 removed outlier: 3.652A pdb=" N GLY B 590 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 322 through 323 removed outlier: 6.767A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 351 through 355 removed outlier: 4.121A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 396 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL B 430 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.782A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 449 through 451 removed outlier: 3.534A pdb=" N TYR B 450 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.658A pdb=" N TYR B 470 " --> pdb=" O TYR B 486 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 548 through 550 Processing sheet with id=AD5, first strand: chain 'B' and resid 651 through 656 removed outlier: 6.386A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N VAL B 653 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 688 " --> pdb=" O GLN B 672 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 672 " --> pdb=" O SER B 688 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 709 through 712 Processing sheet with id=AD7, first strand: chain 'B' and resid 715 through 725 removed outlier: 3.752A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 722 " --> pdb=" O PHE B1059 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 732 through 733 Processing sheet with id=AD9, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.577A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B1079 " --> pdb=" O VAL B1130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1091 through 1094 removed outlier: 3.626A pdb=" N VAL B1091 " --> pdb=" O THR B1102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.764A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C 261 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER C 200 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.734A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 163 through 166 removed outlier: 3.723A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE C 103 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN C 236 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 308 through 311 removed outlier: 3.622A pdb=" N THR C 596 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 609 " --> pdb=" O CYS C 646 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N CYS C 646 " --> pdb=" O TYR C 609 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 321 through 325 removed outlier: 3.808A pdb=" N PHE C 540 " --> pdb=" O LEU C 543 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.959A pdb=" N ASN C 351 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER C 396 " --> pdb=" O ASN C 351 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA C 394 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE C 355 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL C 430 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS C 375 " --> pdb=" O VAL C 430 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 432 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR C 373 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.442A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF1, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF2, first strand: chain 'C' and resid 548 through 551 removed outlier: 3.681A pdb=" N THR C 585 " --> pdb=" O VAL C 548 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 550 " --> pdb=" O ASP C 583 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 573 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 651 through 657 removed outlier: 6.090A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N VAL C 653 " --> pdb=" O THR C 693 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 708 through 712 removed outlier: 4.803A pdb=" N GLN C1103 " --> pdb=" O GLU C1108 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLU C1108 " --> pdb=" O GLN C1103 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 715 through 725 removed outlier: 7.268A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AF7, first strand: chain 'C' and resid 1078 through 1079 removed outlier: 4.776A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C1120 " --> pdb=" O ALA C1084 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AF9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.498A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.682A pdb=" N TYR H 108 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.558A pdb=" N VAL L 11 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TRP L 38 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 19 through 24 916 hydrogen bonds defined for protein. 2418 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: 13.56 Time building geometry restraints manager: 13.65 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: 8970 1.34 - 1.46: 7204 1.46 - 1.59: 12914 1.59 - 1.71: 0 1.71 - 1.83: 155 Bond restraints: 29243 Sorted by residual: bond pdb=" N GLN A 318 " pdb=" CA GLN A 318 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.90e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" N ILE B 323 " pdb=" CA ILE B 323 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.11e-02 8.12e+03 1.52e+01 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N ILE A 329 " pdb=" CA ILE A 329 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.18e+01 ... (remaining 29238 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.97: 667 105.97 - 113.05: 16019 113.05 - 120.14: 9873 120.14 - 127.23: 12956 127.23 - 134.32: 265 Bond angle restraints: 39780 Sorted by residual: angle pdb=" N PHE C 104 " pdb=" CA PHE C 104 " pdb=" C PHE C 104 " ideal model delta sigma weight residual 108.55 115.41 -6.86 1.62e+00 3.81e-01 1.79e+01 angle pdb=" N VAL B 207 " pdb=" CA VAL B 207 " pdb=" C VAL B 207 " ideal model delta sigma weight residual 106.21 110.72 -4.51 1.07e+00 8.73e-01 1.78e+01 angle pdb=" CA ILE A 329 " pdb=" C ILE A 329 " pdb=" O ILE A 329 " ideal model delta sigma weight residual 121.63 117.65 3.98 9.90e-01 1.02e+00 1.62e+01 angle pdb=" N PHE A 303 " pdb=" CA PHE A 303 " pdb=" C PHE A 303 " ideal model delta sigma weight residual 114.31 109.20 5.11 1.29e+00 6.01e-01 1.57e+01 angle pdb=" CA ASN A 328 " pdb=" C ASN A 328 " pdb=" O ASN A 328 " ideal model delta sigma weight residual 122.37 118.01 4.36 1.15e+00 7.56e-01 1.44e+01 ... (remaining 39775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.79: 17341 24.79 - 49.58: 826 49.58 - 74.37: 83 74.37 - 99.16: 46 99.16 - 123.95: 24 Dihedral angle restraints: 18320 sinusoidal: 8047 harmonic: 10273 Sorted by residual: dihedral pdb=" CB CYS A 735 " pdb=" SG CYS A 735 " pdb=" SG CYS A 757 " pdb=" CB CYS A 757 " ideal model delta sinusoidal sigma weight residual -86.00 -4.22 -81.78 1 1.00e+01 1.00e-02 8.23e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 91 " pdb=" CB CYS L 91 " ideal model delta sinusoidal sigma weight residual 93.00 23.80 69.20 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CB CYS A 740 " pdb=" SG CYS A 740 " pdb=" SG CYS A 746 " pdb=" CB CYS A 746 " ideal model delta sinusoidal sigma weight residual -86.00 -24.54 -61.46 1 1.00e+01 1.00e-02 5.01e+01 ... (remaining 18317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 4585 0.117 - 0.234: 99 0.234 - 0.351: 7 0.351 - 0.468: 0 0.468 - 0.585: 1 Chirality restraints: 4692 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 328 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.55e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A1071 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C5 BMA W 3 " pdb=" C4 BMA W 3 " pdb=" C6 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 4689 not shown) Planarity restraints: 5073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 321 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C GLU B 321 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU B 321 " -0.017 2.00e-02 2.50e+03 pdb=" N SER B 322 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 706 " -0.022 2.00e-02 2.50e+03 2.01e-02 5.05e+00 pdb=" CG ASN B 706 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 706 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 706 " 0.017 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 557 " -0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO A 558 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 558 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 558 " -0.027 5.00e-02 4.00e+02 ... (remaining 5070 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 15 2.26 - 2.92: 12490 2.92 - 3.58: 39725 3.58 - 4.24: 62145 4.24 - 4.90: 103968 Nonbonded interactions: 218343 Sorted by model distance: nonbonded pdb=" OG SER A 443 " pdb=" NE ARG H 60 " model vdw 1.600 2.520 nonbonded pdb=" CB SER A 443 " pdb=" NE ARG H 60 " model vdw 1.947 3.520 nonbonded pdb=" O ASN B 367 " pdb=" OH TYR C 486 " model vdw 2.065 2.440 nonbonded pdb=" OG1 THR L 95 " pdb=" O SER L 98 " model vdw 2.127 2.440 nonbonded pdb=" O PRO C1140 " pdb=" OG SER C1144 " model vdw 2.166 2.440 ... (remaining 218338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 1159 or resid 1301 through 1308)) selection = (chain 'C' and (resid 14 through 1159 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'Q' selection = chain 'W' selection = chain 'X' } 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: 2.680 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: 11.630 Check model and map are aligned: 0.410 Set scattering table: 0.270 Process input model: 80.640 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.350 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 0.082 29243 Z= 0.257 Angle : 0.663 10.450 39780 Z= 0.350 Chirality : 0.048 0.585 4692 Planarity : 0.004 0.069 5032 Dihedral : 14.729 123.949 11585 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 0.26 % Allowed : 0.52 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3488 helix: -0.08 (0.21), residues: 659 sheet: -0.37 (0.20), residues: 708 loop : -1.66 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 109 HIS 0.011 0.001 HIS A 622 PHE 0.018 0.001 PHE C 104 TYR 0.021 0.001 TYR C 450 ARG 0.006 0.000 ARG B 574 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 175 time to evaluate : 3.478 Fit side-chains revert: symmetry clash REVERT: A 215 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7882 (mm-40) REVERT: A 742 ASP cc_start: 0.6922 (p0) cc_final: 0.6382 (t0) REVERT: B 377 TYR cc_start: 0.6299 (m-10) cc_final: 0.6090 (m-10) REVERT: B 448 TYR cc_start: 0.6210 (m-10) cc_final: 0.5313 (m-80) REVERT: B 1143 ASP cc_start: 0.9071 (m-30) cc_final: 0.8812 (p0) REVERT: L 52 TYR cc_start: 0.8169 (p90) cc_final: 0.7835 (p90) outliers start: 8 outliers final: 2 residues processed: 183 average time/residue: 0.4140 time to fit residues: 121.4010 Evaluate side-chains 117 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 141 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 146 optimal weight: 30.0000 chunk 90 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 chunk 272 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 203 optimal weight: 3.9990 chunk 316 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 HIS B 759 GLN B 781 GLN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN C 406 GLN C 923 GLN C 962 GLN C1007 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 29243 Z= 0.389 Angle : 0.722 9.514 39780 Z= 0.369 Chirality : 0.049 0.542 4692 Planarity : 0.005 0.048 5032 Dihedral : 9.589 108.265 5224 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.77 % Favored : 93.21 % Rotamer: Outliers : 1.07 % Allowed : 8.71 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.13), residues: 3488 helix: -0.18 (0.19), residues: 712 sheet: -0.56 (0.19), residues: 721 loop : -1.80 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 109 HIS 0.007 0.002 HIS B 202 PHE 0.028 0.002 PHE B 196 TYR 0.025 0.002 TYR A 393 ARG 0.012 0.001 ARG B1104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 3.460 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.7206 (m-80) REVERT: A 148 MET cc_start: 0.7647 (mmm) cc_final: 0.7413 (mmm) REVERT: A 633 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.6357 (t80) REVERT: A 742 ASP cc_start: 0.7008 (p0) cc_final: 0.6476 (t0) REVERT: B 314 ASN cc_start: 0.7515 (t0) cc_final: 0.7260 (t0) REVERT: B 377 TYR cc_start: 0.6275 (m-10) cc_final: 0.6046 (m-10) REVERT: B 448 TYR cc_start: 0.6402 (m-10) cc_final: 0.5498 (m-80) REVERT: B 737 MET cc_start: 0.8995 (tpt) cc_final: 0.8697 (tpp) REVERT: C 119 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7667 (t0) REVERT: C 424 ASP cc_start: 0.8732 (m-30) cc_final: 0.8523 (m-30) REVERT: C 633 TYR cc_start: 0.8088 (t80) cc_final: 0.7857 (t80) REVERT: C 897 MET cc_start: 0.8856 (ppp) cc_final: 0.8650 (ppp) REVERT: H 84 MET cc_start: 0.8324 (tpt) cc_final: 0.8029 (tpt) outliers start: 33 outliers final: 20 residues processed: 155 average time/residue: 0.3693 time to fit residues: 97.0791 Evaluate side-chains 135 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 3.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1047 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 263 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 316 optimal weight: 0.9990 chunk 342 optimal weight: 4.9990 chunk 281 optimal weight: 8.9990 chunk 313 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 253 optimal weight: 0.0060 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 HIS ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29243 Z= 0.241 Angle : 0.607 11.067 39780 Z= 0.307 Chirality : 0.045 0.502 4692 Planarity : 0.004 0.047 5032 Dihedral : 8.072 103.367 5224 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.65 % Allowed : 11.44 % Favored : 86.91 % 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: -1.62 (0.14), residues: 3488 helix: -0.01 (0.20), residues: 719 sheet: -0.46 (0.19), residues: 736 loop : -1.77 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 109 HIS 0.004 0.001 HIS B 202 PHE 0.021 0.001 PHE B 133 TYR 0.021 0.001 TYR A 393 ARG 0.007 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 124 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.7139 (m-80) REVERT: A 191 ASN cc_start: 0.6686 (OUTLIER) cc_final: 0.6195 (t0) REVERT: A 318 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7967 (mp10) REVERT: A 633 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.6197 (t80) REVERT: A 742 ASP cc_start: 0.6962 (p0) cc_final: 0.6490 (t0) REVERT: B 84 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7277 (t80) REVERT: B 314 ASN cc_start: 0.7439 (t0) cc_final: 0.7192 (t0) REVERT: B 448 TYR cc_start: 0.6449 (m-10) cc_final: 0.5538 (m-80) REVERT: B 737 MET cc_start: 0.8966 (tpt) cc_final: 0.8719 (tpp) REVERT: B 999 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8377 (tm-30) REVERT: C 633 TYR cc_start: 0.7949 (t80) cc_final: 0.7647 (t80) REVERT: C 737 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7980 (ttp) REVERT: C 777 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8366 (mt-10) REVERT: C 897 MET cc_start: 0.8844 (ppp) cc_final: 0.8521 (ppp) REVERT: H 84 MET cc_start: 0.8191 (tpt) cc_final: 0.7987 (tpt) REVERT: H 87 MET cc_start: 0.5145 (pmm) cc_final: 0.4663 (pmm) outliers start: 51 outliers final: 30 residues processed: 163 average time/residue: 0.3717 time to fit residues: 102.6212 Evaluate side-chains 146 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 110 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1143 ASP Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 0.8980 chunk 238 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 151 optimal weight: 30.0000 chunk 212 optimal weight: 4.9990 chunk 317 optimal weight: 3.9990 chunk 336 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 301 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN H 86 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29243 Z= 0.183 Angle : 0.573 11.721 39780 Z= 0.288 Chirality : 0.044 0.489 4692 Planarity : 0.004 0.049 5032 Dihedral : 6.949 97.946 5222 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.78 % Allowed : 13.12 % Favored : 85.10 % 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: -1.46 (0.14), residues: 3488 helix: 0.14 (0.20), residues: 724 sheet: -0.32 (0.19), residues: 748 loop : -1.70 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 109 HIS 0.003 0.001 HIS A 141 PHE 0.022 0.001 PHE B1145 TYR 0.022 0.001 TYR A 393 ARG 0.004 0.000 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 129 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.7003 (m-80) REVERT: A 633 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.6408 (t80) REVERT: A 742 ASP cc_start: 0.6832 (p0) cc_final: 0.6279 (t0) REVERT: A 985 GLU cc_start: 0.8593 (pm20) cc_final: 0.8263 (pm20) REVERT: B 84 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.6837 (t80) REVERT: B 314 ASN cc_start: 0.7464 (t0) cc_final: 0.7215 (t0) REVERT: B 377 TYR cc_start: 0.6397 (m-80) cc_final: 0.6137 (m-10) REVERT: B 448 TYR cc_start: 0.6469 (m-10) cc_final: 0.5552 (m-80) REVERT: B 737 MET cc_start: 0.8959 (tpt) cc_final: 0.8739 (tpp) REVERT: B 777 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7916 (mt-10) REVERT: B 999 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8246 (tm-30) REVERT: C 126 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8620 (mm) REVERT: C 633 TYR cc_start: 0.7853 (t80) cc_final: 0.7610 (t80) REVERT: C 897 MET cc_start: 0.8854 (ppp) cc_final: 0.8491 (ppp) outliers start: 55 outliers final: 31 residues processed: 175 average time/residue: 0.3485 time to fit residues: 104.1347 Evaluate side-chains 152 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 287 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 171 optimal weight: 5.9990 chunk 301 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29243 Z= 0.314 Angle : 0.642 11.751 39780 Z= 0.324 Chirality : 0.046 0.513 4692 Planarity : 0.004 0.051 5032 Dihedral : 6.886 93.252 5222 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.46 % Allowed : 14.87 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.14), residues: 3488 helix: 0.07 (0.20), residues: 735 sheet: -0.47 (0.19), residues: 747 loop : -1.78 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 109 HIS 0.006 0.001 HIS B 202 PHE 0.026 0.002 PHE C 756 TYR 0.023 0.001 TYR A 393 ARG 0.005 0.001 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 115 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8287 (tp) REVERT: A 133 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6974 (m-80) REVERT: A 318 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8045 (mp10) REVERT: A 633 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.6475 (t80) REVERT: A 983 LYS cc_start: 0.8105 (pttt) cc_final: 0.6838 (mmtm) REVERT: B 84 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7155 (t80) REVERT: B 314 ASN cc_start: 0.7379 (t0) cc_final: 0.7070 (t0) REVERT: B 448 TYR cc_start: 0.6553 (m-10) cc_final: 0.5689 (m-80) REVERT: B 737 MET cc_start: 0.8978 (tpt) cc_final: 0.8765 (tpp) REVERT: B 999 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8359 (tm-30) REVERT: C 126 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8718 (mm) REVERT: C 463 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8536 (tpp-160) REVERT: C 633 TYR cc_start: 0.8088 (t80) cc_final: 0.7757 (t80) REVERT: C 737 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8059 (ttm) REVERT: C 777 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8352 (mt-10) REVERT: C 897 MET cc_start: 0.9015 (ppp) cc_final: 0.8624 (ppp) REVERT: H 34 VAL cc_start: 0.8724 (t) cc_final: 0.7255 (t) REVERT: H 84 MET cc_start: 0.8576 (tpt) cc_final: 0.8338 (tpt) REVERT: L 52 TYR cc_start: 0.8130 (p90) cc_final: 0.7832 (p90) outliers start: 76 outliers final: 50 residues processed: 179 average time/residue: 0.3710 time to fit residues: 112.6349 Evaluate side-chains 164 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 106 time to evaluate : 3.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1143 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 814 PHE Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 8.9990 chunk 302 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 336 optimal weight: 10.0000 chunk 279 optimal weight: 3.9990 chunk 155 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29243 Z= 0.229 Angle : 0.590 10.284 39780 Z= 0.297 Chirality : 0.044 0.501 4692 Planarity : 0.004 0.054 5032 Dihedral : 6.549 89.988 5222 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.66 % Allowed : 15.65 % Favored : 81.70 % 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: -1.53 (0.14), residues: 3488 helix: 0.14 (0.20), residues: 751 sheet: -0.35 (0.19), residues: 752 loop : -1.81 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 255 HIS 0.005 0.001 HIS B 141 PHE 0.043 0.001 PHE L 103 TYR 0.022 0.001 TYR A 393 ARG 0.014 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 116 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8480 (tp) REVERT: A 133 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: A 318 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8004 (mp10) REVERT: A 633 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.6464 (t80) REVERT: B 84 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7086 (t80) REVERT: B 195 TYR cc_start: 0.8314 (m-80) cc_final: 0.8008 (t80) REVERT: B 314 ASN cc_start: 0.7301 (t0) cc_final: 0.7036 (t0) REVERT: B 448 TYR cc_start: 0.6549 (m-10) cc_final: 0.5684 (m-80) REVERT: B 633 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.6226 (t80) REVERT: B 999 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8292 (tm-30) REVERT: C 212 ASP cc_start: 0.6279 (OUTLIER) cc_final: 0.6068 (m-30) REVERT: C 463 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8647 (tpp-160) REVERT: C 633 TYR cc_start: 0.7989 (t80) cc_final: 0.7657 (t80) REVERT: C 737 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.8010 (ttm) REVERT: C 777 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8385 (mt-10) REVERT: C 897 MET cc_start: 0.8972 (ppp) cc_final: 0.8577 (ppp) REVERT: H 84 MET cc_start: 0.8460 (tpt) cc_final: 0.8242 (tpt) REVERT: H 87 MET cc_start: 0.5116 (pmm) cc_final: 0.4773 (pmm) REVERT: H 106 PHE cc_start: 0.7858 (m-80) cc_final: 0.7429 (m-80) REVERT: L 52 TYR cc_start: 0.8067 (p90) cc_final: 0.7778 (p90) outliers start: 82 outliers final: 55 residues processed: 186 average time/residue: 0.3589 time to fit residues: 113.9092 Evaluate side-chains 174 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 110 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 906 ILE Chi-restraints excluded: chain C residue 1105 ASN Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 191 optimal weight: 0.9990 chunk 245 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 335 optimal weight: 8.9990 chunk 209 optimal weight: 0.0010 chunk 204 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29243 Z= 0.234 Angle : 0.593 10.911 39780 Z= 0.297 Chirality : 0.044 0.497 4692 Planarity : 0.004 0.052 5032 Dihedral : 6.326 84.571 5222 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.79 % Allowed : 16.55 % Favored : 80.66 % 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 (0.14), residues: 3488 helix: 0.23 (0.20), residues: 747 sheet: -0.33 (0.19), residues: 744 loop : -1.82 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 109 HIS 0.004 0.001 HIS B 202 PHE 0.032 0.001 PHE B 196 TYR 0.016 0.001 TYR B1152 ARG 0.005 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 110 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8522 (tp) REVERT: A 133 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: A 318 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8005 (mp10) REVERT: A 633 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.6454 (t80) REVERT: B 84 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7101 (t80) REVERT: B 195 TYR cc_start: 0.8214 (m-80) cc_final: 0.7983 (t80) REVERT: B 314 ASN cc_start: 0.7402 (t0) cc_final: 0.7155 (t0) REVERT: B 448 TYR cc_start: 0.6557 (m-10) cc_final: 0.5694 (m-80) REVERT: B 633 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.6206 (t80) REVERT: B 706 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8072 (p0) REVERT: B 999 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8272 (tm-30) REVERT: C 212 ASP cc_start: 0.6356 (OUTLIER) cc_final: 0.6147 (m-30) REVERT: C 463 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8630 (tpp-160) REVERT: C 633 TYR cc_start: 0.8059 (t80) cc_final: 0.7701 (t80) REVERT: C 737 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.8013 (ttm) REVERT: C 749 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9320 (tt) REVERT: C 777 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8355 (mt-10) REVERT: C 897 MET cc_start: 0.9000 (ppp) cc_final: 0.8605 (ppp) REVERT: H 84 MET cc_start: 0.8505 (tpt) cc_final: 0.8274 (tpt) outliers start: 86 outliers final: 64 residues processed: 181 average time/residue: 0.3559 time to fit residues: 110.5249 Evaluate side-chains 182 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 107 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 170 PHE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1105 ASN Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 213 optimal weight: 0.0050 chunk 228 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 263 optimal weight: 9.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 ASN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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 : 0.004 0.050 29243 Z= 0.230 Angle : 0.593 11.456 39780 Z= 0.296 Chirality : 0.044 0.496 4692 Planarity : 0.004 0.052 5032 Dihedral : 6.218 80.133 5222 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.57 % Favored : 93.41 % Rotamer: Outliers : 3.05 % Allowed : 16.59 % Favored : 80.37 % 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: -1.47 (0.14), residues: 3488 helix: 0.33 (0.20), residues: 745 sheet: -0.34 (0.19), residues: 746 loop : -1.81 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 109 HIS 0.004 0.001 HIS B 202 PHE 0.027 0.001 PHE C 756 TYR 0.017 0.001 TYR A 393 ARG 0.007 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 113 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8591 (tp) REVERT: A 133 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6835 (m-80) REVERT: A 458 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8264 (pp) REVERT: A 633 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.6522 (t80) REVERT: B 84 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7176 (t80) REVERT: B 314 ASN cc_start: 0.7624 (t0) cc_final: 0.7357 (t0) REVERT: B 448 TYR cc_start: 0.6570 (m-10) cc_final: 0.5726 (m-80) REVERT: B 633 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.6128 (t80) REVERT: B 706 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8109 (p0) REVERT: B 999 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8264 (tm-30) REVERT: C 116 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8203 (tp) REVERT: C 212 ASP cc_start: 0.6340 (OUTLIER) cc_final: 0.6136 (m-30) REVERT: C 463 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8635 (tpp-160) REVERT: C 633 TYR cc_start: 0.8060 (t80) cc_final: 0.7630 (t80) REVERT: C 737 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7986 (ttm) REVERT: C 749 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9321 (tt) REVERT: C 777 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8385 (mt-10) REVERT: C 897 MET cc_start: 0.8976 (ppp) cc_final: 0.8592 (ppp) REVERT: C 1047 MET cc_start: 0.7964 (ptp) cc_final: 0.7697 (mtm) REVERT: H 84 MET cc_start: 0.8642 (tpt) cc_final: 0.8337 (tpt) REVERT: L 52 TYR cc_start: 0.8076 (p90) cc_final: 0.7775 (p90) outliers start: 94 outliers final: 65 residues processed: 193 average time/residue: 0.3544 time to fit residues: 117.8246 Evaluate side-chains 182 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 105 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1105 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 2.9990 chunk 321 optimal weight: 7.9990 chunk 293 optimal weight: 6.9990 chunk 312 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 282 optimal weight: 6.9990 chunk 295 optimal weight: 3.9990 chunk 311 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29243 Z= 0.215 Angle : 0.593 14.046 39780 Z= 0.294 Chirality : 0.044 0.492 4692 Planarity : 0.004 0.063 5032 Dihedral : 6.119 76.743 5222 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.54 % Favored : 93.43 % Rotamer: Outliers : 2.82 % Allowed : 16.91 % Favored : 80.27 % 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: -1.43 (0.14), residues: 3488 helix: 0.40 (0.20), residues: 747 sheet: -0.31 (0.19), residues: 754 loop : -1.81 (0.13), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 883 HIS 0.004 0.001 HIS B 202 PHE 0.032 0.001 PHE H 27 TYR 0.020 0.001 TYR B1152 ARG 0.013 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 116 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6830 (m-80) REVERT: A 458 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8258 (pp) REVERT: A 633 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.6575 (t80) REVERT: B 84 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7279 (t80) REVERT: B 314 ASN cc_start: 0.7618 (t0) cc_final: 0.7353 (t0) REVERT: B 448 TYR cc_start: 0.6519 (m-10) cc_final: 0.5626 (m-80) REVERT: B 633 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.6139 (t80) REVERT: B 706 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8107 (p0) REVERT: B 721 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.9151 (p) REVERT: B 999 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8249 (tm-30) REVERT: C 116 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8170 (tp) REVERT: C 463 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8646 (tpp-160) REVERT: C 633 TYR cc_start: 0.7971 (t80) cc_final: 0.7491 (t80) REVERT: C 737 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7993 (ttm) REVERT: C 777 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8323 (mt-10) REVERT: C 897 MET cc_start: 0.8970 (ppp) cc_final: 0.8580 (ppp) REVERT: C 999 GLN cc_start: 0.8547 (tt0) cc_final: 0.8210 (tm-30) REVERT: H 84 MET cc_start: 0.8603 (tpt) cc_final: 0.8177 (tpt) REVERT: H 87 MET cc_start: 0.5105 (pmm) cc_final: 0.4658 (pmm) REVERT: L 52 TYR cc_start: 0.8064 (p90) cc_final: 0.7770 (p90) outliers start: 87 outliers final: 66 residues processed: 189 average time/residue: 0.3481 time to fit residues: 114.0993 Evaluate side-chains 185 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 109 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1105 ASN Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 5.9990 chunk 330 optimal weight: 20.0000 chunk 201 optimal weight: 1.9990 chunk 156 optimal weight: 50.0000 chunk 229 optimal weight: 10.0000 chunk 346 optimal weight: 7.9990 chunk 319 optimal weight: 0.7980 chunk 276 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 213 optimal weight: 0.2980 chunk 169 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN A 687 GLN ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29243 Z= 0.175 Angle : 0.580 14.740 39780 Z= 0.287 Chirality : 0.044 0.479 4692 Planarity : 0.004 0.052 5032 Dihedral : 5.872 73.154 5222 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.79 % Favored : 94.15 % Rotamer: Outliers : 2.59 % Allowed : 17.01 % Favored : 80.40 % 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: -1.33 (0.14), residues: 3488 helix: 0.47 (0.20), residues: 747 sheet: -0.21 (0.19), residues: 740 loop : -1.75 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP H 109 HIS 0.007 0.001 HIS L 41 PHE 0.031 0.001 PHE B 756 TYR 0.022 0.001 TYR A 393 ARG 0.011 0.000 ARG H 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 116 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: A 458 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8279 (pp) REVERT: A 633 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.6517 (t80) REVERT: B 84 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7247 (t80) REVERT: B 314 ASN cc_start: 0.7563 (t0) cc_final: 0.7315 (t0) REVERT: B 448 TYR cc_start: 0.6444 (m-10) cc_final: 0.5520 (m-80) REVERT: B 633 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.6068 (t80) REVERT: B 706 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8132 (p0) REVERT: B 721 THR cc_start: 0.9352 (OUTLIER) cc_final: 0.9147 (p) REVERT: B 777 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7803 (mt-10) REVERT: B 999 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8198 (tm-30) REVERT: C 116 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8097 (tp) REVERT: C 335 PHE cc_start: 0.8766 (m-80) cc_final: 0.8564 (m-10) REVERT: C 463 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8663 (tpp-160) REVERT: C 633 TYR cc_start: 0.7943 (t80) cc_final: 0.7470 (t80) REVERT: C 737 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7937 (ttm) REVERT: C 897 MET cc_start: 0.8935 (ppp) cc_final: 0.8548 (ppp) REVERT: C 999 GLN cc_start: 0.8503 (tt0) cc_final: 0.8160 (tm-30) REVERT: H 84 MET cc_start: 0.8610 (tpt) cc_final: 0.8395 (tpt) REVERT: L 52 TYR cc_start: 0.8080 (p90) cc_final: 0.7774 (p90) outliers start: 80 outliers final: 59 residues processed: 183 average time/residue: 0.3804 time to fit residues: 120.1717 Evaluate side-chains 182 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 113 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1105 ASN Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 5.9990 chunk 294 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 254 optimal weight: 0.5980 chunk 40 optimal weight: 0.0770 chunk 76 optimal weight: 8.9990 chunk 276 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 283 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 HIS ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.072551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.049571 restraints weight = 139657.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.051092 restraints weight = 70130.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.052050 restraints weight = 46049.956| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29243 Z= 0.151 Angle : 0.569 14.676 39780 Z= 0.279 Chirality : 0.044 0.472 4692 Planarity : 0.004 0.051 5032 Dihedral : 5.631 69.379 5222 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.42 % Favored : 94.52 % Rotamer: Outliers : 2.27 % Allowed : 17.30 % Favored : 80.43 % 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: -1.24 (0.14), residues: 3488 helix: 0.54 (0.20), residues: 747 sheet: -0.08 (0.19), residues: 733 loop : -1.71 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 109 HIS 0.004 0.001 HIS B1080 PHE 0.032 0.001 PHE B 756 TYR 0.021 0.001 TYR A 393 ARG 0.010 0.000 ARG H 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4457.09 seconds wall clock time: 84 minutes 6.41 seconds (5046.41 seconds total)