Starting phenix.real_space_refine on Tue Feb 20 06:52:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z86_14544/02_2024/7z86_14544.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z86_14544/02_2024/7z86_14544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z86_14544/02_2024/7z86_14544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z86_14544/02_2024/7z86_14544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z86_14544/02_2024/7z86_14544.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z86_14544/02_2024/7z86_14544.pdb" } resolution = 3.4 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= 0.005 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 120 5.16 5 C 17216 2.51 5 N 4414 2.21 5 O 5321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "X GLU 100": "OE1" <-> "OE2" Residue "Y GLU 100": "OE1" <-> "OE2" Residue "Z GLU 100": "OE1" <-> "OE2" 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: 27071 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7712 Classifications: {'peptide': 987} Link IDs: {'PTRANS': 49, 'TRANS': 937} Chain breaks: 9 Chain: "B" Number of atoms: 7745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7745 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Chain: "C" Number of atoms: 7738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7738 Classifications: {'peptide': 991} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Chain: "X" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "Y" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "Z" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.40, per 1000 atoms: 0.49 Number of scatterers: 27071 At special positions: 0 Unit cell: (128.64, 136.144, 214.4, 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 120 16.00 O 5321 8.00 N 4414 7.00 C 17216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.01 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.06 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.07 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.07 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.06 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.01 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.01 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 61 " " NAG C1403 " - " ASN C 234 " " NAG C1404 " - " ASN C 331 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " ASN C 165 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 122 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C 709 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Time building additional restraints: 9.97 Conformation dependent library (CDL) restraints added in 6.2 seconds 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6244 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 55 sheets defined 25.0% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.959A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.188A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.350A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.602A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.216A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.935A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 4.008A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.670A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.954A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.331A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.083A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.827A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.259A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.671A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.523A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.616A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.283A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.021A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.084A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.060A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.563A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.673A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.248A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.609A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.555A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.065A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.158A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 65 Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'X' and resid 105 through 111 Processing helix chain 'Y' and resid 62 through 65 Processing helix chain 'Y' and resid 87 through 91 Processing helix chain 'Y' and resid 105 through 111 Processing helix chain 'Z' and resid 62 through 65 Processing helix chain 'Z' and resid 87 through 91 Processing helix chain 'Z' and resid 105 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.675A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.333A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.542A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.646A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.545A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.452A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.084A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.933A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.705A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.983A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.194A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.720A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.426A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.268A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.725A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.683A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.602A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.889A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.983A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 719 through 728 removed outlier: 6.030A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.240A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.538A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.444A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.707A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.959A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.574A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.119A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.209A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.011A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.974A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 719 through 728 removed outlier: 7.000A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.132A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.550A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 3 through 8 Processing sheet with id=AF3, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.301A pdb=" N GLY X 10 " --> pdb=" O THR X 124 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N SER X 126 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET X 12 " --> pdb=" O SER X 126 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG X 38 " --> pdb=" O PHE X 47 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N PHE X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.301A pdb=" N GLY X 10 " --> pdb=" O THR X 124 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N SER X 126 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET X 12 " --> pdb=" O SER X 126 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 3 through 8 Processing sheet with id=AF6, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.301A pdb=" N GLY Y 10 " --> pdb=" O THR Y 124 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N SER Y 126 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET Y 12 " --> pdb=" O SER Y 126 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG Y 38 " --> pdb=" O PHE Y 47 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N PHE Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.301A pdb=" N GLY Y 10 " --> pdb=" O THR Y 124 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N SER Y 126 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET Y 12 " --> pdb=" O SER Y 126 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 3 through 8 Processing sheet with id=AF9, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.301A pdb=" N GLY Z 10 " --> pdb=" O THR Z 124 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N SER Z 126 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET Z 12 " --> pdb=" O SER Z 126 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG Z 38 " --> pdb=" O PHE Z 47 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE Z 47 " --> pdb=" O ARG Z 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.301A pdb=" N GLY Z 10 " --> pdb=" O THR Z 124 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N SER Z 126 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET Z 12 " --> pdb=" O SER Z 126 " (cutoff:3.500A) 1168 hydrogen bonds defined for protein. 3090 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: 13.48 Time building geometry restraints manager: 10.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5205 1.33 - 1.46: 9895 1.46 - 1.59: 12409 1.59 - 1.72: 0 1.72 - 1.84: 153 Bond restraints: 27662 Sorted by residual: bond pdb=" CE1 HIS B 49 " pdb=" NE2 HIS B 49 " ideal model delta sigma weight residual 1.321 1.351 -0.030 1.00e-02 1.00e+04 9.19e+00 bond pdb=" CA SER A 325 " pdb=" CB SER A 325 " ideal model delta sigma weight residual 1.531 1.486 0.045 1.52e-02 4.33e+03 8.77e+00 bond pdb=" CE1 HIS C1058 " pdb=" NE2 HIS C1058 " ideal model delta sigma weight residual 1.321 1.350 -0.029 1.00e-02 1.00e+04 8.38e+00 bond pdb=" C ASN A 81 " pdb=" N PRO A 82 " ideal model delta sigma weight residual 1.328 1.365 -0.036 1.26e-02 6.30e+03 8.27e+00 bond pdb=" CE1 HIS B1101 " pdb=" NE2 HIS B1101 " ideal model delta sigma weight residual 1.321 1.349 -0.028 1.00e-02 1.00e+04 8.07e+00 ... (remaining 27657 not shown) Histogram of bond angle deviations from ideal: 96.38 - 104.03: 380 104.03 - 111.69: 11172 111.69 - 119.35: 11382 119.35 - 127.01: 14527 127.01 - 134.66: 153 Bond angle restraints: 37614 Sorted by residual: angle pdb=" CA PHE B 565 " pdb=" CB PHE B 565 " pdb=" CG PHE B 565 " ideal model delta sigma weight residual 113.80 120.06 -6.26 1.00e+00 1.00e+00 3.91e+01 angle pdb=" C LYS A 113 " pdb=" CA LYS A 113 " pdb=" CB LYS A 113 " ideal model delta sigma weight residual 110.06 118.90 -8.84 1.44e+00 4.82e-01 3.77e+01 angle pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " pdb=" CG ASP C 198 " ideal model delta sigma weight residual 112.60 118.02 -5.42 1.00e+00 1.00e+00 2.93e+01 angle pdb=" CA PHE B 86 " pdb=" CB PHE B 86 " pdb=" CG PHE B 86 " ideal model delta sigma weight residual 113.80 119.08 -5.28 1.00e+00 1.00e+00 2.79e+01 angle pdb=" C ASN A 81 " pdb=" CA ASN A 81 " pdb=" CB ASN A 81 " ideal model delta sigma weight residual 110.10 119.36 -9.26 1.90e+00 2.77e-01 2.38e+01 ... (remaining 37609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.79: 16187 20.79 - 41.57: 770 41.57 - 62.35: 220 62.35 - 83.14: 48 83.14 - 103.92: 48 Dihedral angle restraints: 17273 sinusoidal: 7549 harmonic: 9724 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.77 79.77 1 1.00e+01 1.00e-02 7.90e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 170.80 -77.80 1 1.00e+01 1.00e-02 7.57e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 168.96 -75.96 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 17270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.630: 4435 0.630 - 1.260: 3 1.260 - 1.889: 0 1.889 - 2.519: 0 2.519 - 3.149: 1 Chirality restraints: 4439 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 0.75 -3.15 2.00e-01 2.50e+01 2.48e+02 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.91e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.11e+02 ... (remaining 4436 not shown) Planarity restraints: 4810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " 0.350 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG A1306 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " 0.140 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " 0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 2 " 0.341 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG U 2 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG U 2 " 0.094 2.00e-02 2.50e+03 pdb=" N2 NAG U 2 " -0.529 2.00e-02 2.50e+03 pdb=" O7 NAG U 2 " 0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.339 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG D 1 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.072 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.522 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.184 2.00e-02 2.50e+03 ... (remaining 4807 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 41 2.41 - 3.03: 16466 3.03 - 3.66: 39261 3.66 - 4.28: 62317 4.28 - 4.90: 103799 Nonbonded interactions: 221884 Sorted by model distance: nonbonded pdb=" O GLN B 613 " pdb=" OD1 ASP B 614 " model vdw 1.791 3.040 nonbonded pdb=" OD1 ASN A 81 " pdb=" CD PRO A 82 " model vdw 1.855 3.440 nonbonded pdb=" CB PHE B 342 " pdb=" O7 NAG B1310 " model vdw 2.118 3.440 nonbonded pdb=" O TRP X 53 " pdb=" CZ ARG X 72 " model vdw 2.123 3.270 nonbonded pdb=" O TRP Y 53 " pdb=" CZ ARG Y 72 " model vdw 2.124 3.270 ... (remaining 221879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 66 or resid 82 through 113 or resid 116 through \ 140 or resid 166 through 263 or resid 265 through 676 or resid 690 through 827 \ or resid 856 through 1147 or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 140 or resid 166 through \ 196 or resid 200 through 211 or resid 215 through 263 or resid 265 through 827 \ or resid 856 through 1147 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 113 or resid 116 through \ 140 or resid 166 through 196 or resid 200 through 211 or resid 215 through 1147 \ or resid 1401 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 7.130 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 72.090 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 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 : 0.008 0.053 27662 Z= 0.527 Angle : 1.193 10.517 37614 Z= 0.752 Chirality : 0.101 3.149 4439 Planarity : 0.023 0.301 4765 Dihedral : 14.675 103.925 10903 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.97 % Allowed : 4.10 % Favored : 93.93 % Cbeta Deviations : 0.10 % 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: -0.77 (0.14), residues: 3288 helix: 0.18 (0.20), residues: 676 sheet: -0.13 (0.17), residues: 789 loop : -0.93 (0.13), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.006 TRP C 104 HIS 0.030 0.006 HIS C 655 PHE 0.041 0.007 PHE B 565 TYR 0.042 0.008 TYR A 904 ARG 0.026 0.003 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 431 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.6495 (p) cc_final: 0.6292 (t) REVERT: A 190 ARG cc_start: 0.6635 (mtt90) cc_final: 0.6016 (mtp180) REVERT: A 298 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6805 (mm-30) REVERT: A 389 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7171 (m-30) REVERT: A 558 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7609 (mmmt) REVERT: A 591 SER cc_start: 0.8260 (t) cc_final: 0.7772 (p) REVERT: A 646 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7413 (mtm180) REVERT: A 654 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6698 (tt0) REVERT: A 661 GLU cc_start: 0.8319 (pm20) cc_final: 0.8036 (pt0) REVERT: A 1050 MET cc_start: 0.8229 (ptt) cc_final: 0.7844 (ptp) REVERT: A 1101 HIS cc_start: 0.6772 (m90) cc_final: 0.6546 (m170) REVERT: B 52 GLN cc_start: 0.7607 (tt0) cc_final: 0.6889 (pp30) REVERT: B 90 VAL cc_start: 0.5423 (OUTLIER) cc_final: 0.4889 (t) REVERT: B 169 GLU cc_start: 0.6165 (tt0) cc_final: 0.5631 (tm-30) REVERT: B 287 ASP cc_start: 0.7332 (t0) cc_final: 0.7006 (m-30) REVERT: B 360 ASN cc_start: 0.7214 (t0) cc_final: 0.6933 (m-40) REVERT: B 564 GLN cc_start: 0.6685 (tp40) cc_final: 0.6151 (mm110) REVERT: B 583 GLU cc_start: 0.7251 (pt0) cc_final: 0.6977 (pt0) REVERT: B 614 ASP cc_start: 0.7428 (p0) cc_final: 0.6949 (t0) REVERT: B 646 ARG cc_start: 0.8179 (ttt90) cc_final: 0.7426 (mmp-170) REVERT: B 661 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7859 (mt-10) REVERT: B 740 MET cc_start: 0.7448 (ttt) cc_final: 0.6959 (mtt) REVERT: B 755 GLN cc_start: 0.6534 (mt0) cc_final: 0.6254 (mm110) REVERT: B 823 PHE cc_start: 0.7417 (m-80) cc_final: 0.7170 (m-80) REVERT: B 935 GLN cc_start: 0.6675 (mt0) cc_final: 0.6342 (mt0) REVERT: B 994 ASP cc_start: 0.7047 (t70) cc_final: 0.6628 (m-30) REVERT: B 995 ARG cc_start: 0.6653 (mtt90) cc_final: 0.6339 (mtm-85) REVERT: B 1050 MET cc_start: 0.8477 (ptt) cc_final: 0.8085 (ptm) REVERT: B 1113 GLN cc_start: 0.7190 (mt0) cc_final: 0.6923 (mm-40) REVERT: C 47 VAL cc_start: 0.7860 (p) cc_final: 0.7612 (m) REVERT: C 82 PRO cc_start: 0.7658 (Cg_endo) cc_final: 0.7446 (Cg_exo) REVERT: C 97 LYS cc_start: 0.5660 (OUTLIER) cc_final: 0.5386 (ttpt) REVERT: C 138 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6769 (t0) REVERT: C 191 GLU cc_start: 0.8107 (pm20) cc_final: 0.7868 (pt0) REVERT: C 224 GLU cc_start: 0.7628 (pm20) cc_final: 0.7187 (mp0) REVERT: C 269 TYR cc_start: 0.7841 (m-80) cc_final: 0.7166 (m-80) REVERT: C 282 ASN cc_start: 0.8174 (m-40) cc_final: 0.7965 (m-40) REVERT: C 307 THR cc_start: 0.8064 (p) cc_final: 0.7746 (t) REVERT: C 309 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7005 (mp0) REVERT: C 317 ASN cc_start: 0.8368 (m-40) cc_final: 0.8123 (m-40) REVERT: C 357 ARG cc_start: 0.7323 (ttt180) cc_final: 0.6889 (ttp-110) REVERT: C 532 ASN cc_start: 0.7052 (t0) cc_final: 0.6716 (p0) REVERT: C 646 ARG cc_start: 0.7829 (tpp80) cc_final: 0.7501 (ttt180) REVERT: C 1037 SER cc_start: 0.9044 (t) cc_final: 0.8824 (p) REVERT: C 1045 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8198 (mptt) REVERT: X 12 MET cc_start: 0.2343 (tpp) cc_final: 0.2050 (tpp) REVERT: Y 83 MET cc_start: 0.3967 (mtp) cc_final: 0.3736 (mtm) outliers start: 57 outliers final: 6 residues processed: 478 average time/residue: 0.4044 time to fit residues: 299.4416 Evaluate side-chains 254 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 243 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 280 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 169 optimal weight: 0.5980 chunk 134 optimal weight: 0.2980 chunk 260 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 301 optimal weight: 8.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 580 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 207 HIS B 314 GLN B 388 ASN B 606 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS B1101 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 607 GLN C 613 GLN C 954 GLN C 957 GLN C 969 ASN C1048 HIS C1119 ASN C1135 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27662 Z= 0.185 Angle : 0.614 10.196 37614 Z= 0.303 Chirality : 0.047 0.311 4439 Planarity : 0.004 0.047 4765 Dihedral : 11.127 98.645 5008 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.66 % Allowed : 7.62 % Favored : 90.72 % 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: -0.00 (0.14), residues: 3288 helix: 1.29 (0.21), residues: 687 sheet: 0.04 (0.17), residues: 828 loop : -0.49 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 53 HIS 0.012 0.001 HIS A 207 PHE 0.025 0.001 PHE B 541 TYR 0.021 0.001 TYR A 369 ARG 0.004 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 259 time to evaluate : 3.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6168 (m-80) cc_final: 0.5829 (m-80) REVERT: A 190 ARG cc_start: 0.7089 (mtt90) cc_final: 0.6234 (mtp180) REVERT: A 237 ARG cc_start: 0.5826 (ttm-80) cc_final: 0.5551 (ttt-90) REVERT: A 278 LYS cc_start: 0.7315 (tttt) cc_final: 0.7032 (ttpp) REVERT: A 298 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6749 (mm-30) REVERT: A 389 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7232 (m-30) REVERT: A 591 SER cc_start: 0.8400 (t) cc_final: 0.7943 (p) REVERT: A 646 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7383 (mtm180) REVERT: A 654 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6611 (tt0) REVERT: A 869 MET cc_start: 0.7603 (mtt) cc_final: 0.7360 (mtp) REVERT: A 1050 MET cc_start: 0.8205 (ptt) cc_final: 0.7846 (ptm) REVERT: A 1101 HIS cc_start: 0.6868 (m90) cc_final: 0.6395 (m170) REVERT: A 1119 ASN cc_start: 0.7395 (m-40) cc_final: 0.7140 (m-40) REVERT: B 52 GLN cc_start: 0.7780 (tt0) cc_final: 0.6802 (pp30) REVERT: B 169 GLU cc_start: 0.6344 (tt0) cc_final: 0.5606 (tm-30) REVERT: B 287 ASP cc_start: 0.7485 (t0) cc_final: 0.7104 (m-30) REVERT: B 360 ASN cc_start: 0.7505 (t0) cc_final: 0.7107 (m-40) REVERT: B 510 VAL cc_start: 0.6857 (t) cc_final: 0.6563 (t) REVERT: B 583 GLU cc_start: 0.7090 (pt0) cc_final: 0.6889 (pt0) REVERT: B 614 ASP cc_start: 0.7420 (p0) cc_final: 0.6858 (m-30) REVERT: B 646 ARG cc_start: 0.8120 (ttt90) cc_final: 0.7421 (mmp-170) REVERT: B 661 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7903 (mt-10) REVERT: B 740 MET cc_start: 0.7683 (ttt) cc_final: 0.7244 (mtp) REVERT: B 755 GLN cc_start: 0.6637 (mt0) cc_final: 0.6260 (mm110) REVERT: B 994 ASP cc_start: 0.6987 (t70) cc_final: 0.6782 (t0) REVERT: B 1045 LYS cc_start: 0.7723 (mmmt) cc_final: 0.7196 (mmtm) REVERT: B 1050 MET cc_start: 0.8513 (ptt) cc_final: 0.8242 (ptm) REVERT: B 1092 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7304 (pp20) REVERT: B 1113 GLN cc_start: 0.7172 (mt0) cc_final: 0.6779 (mm-40) REVERT: C 97 LYS cc_start: 0.5377 (OUTLIER) cc_final: 0.5112 (ttpt) REVERT: C 138 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6604 (t0) REVERT: C 309 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6758 (mp0) REVERT: C 357 ARG cc_start: 0.7268 (ttt180) cc_final: 0.6963 (ttp-110) REVERT: C 532 ASN cc_start: 0.7150 (t0) cc_final: 0.6662 (p0) REVERT: C 646 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7503 (ttt-90) REVERT: C 964 LYS cc_start: 0.7544 (mmmt) cc_final: 0.7238 (mtmt) REVERT: C 1045 LYS cc_start: 0.8631 (mtpp) cc_final: 0.8117 (mptt) REVERT: C 1050 MET cc_start: 0.8608 (ptm) cc_final: 0.8340 (ptp) REVERT: X 12 MET cc_start: 0.2204 (tpp) cc_final: 0.1897 (tpp) REVERT: X 34 MET cc_start: 0.3372 (mmm) cc_final: 0.3004 (ptt) REVERT: Y 83 MET cc_start: 0.3639 (mtp) cc_final: 0.3436 (mtm) outliers start: 48 outliers final: 29 residues processed: 291 average time/residue: 0.3929 time to fit residues: 183.1667 Evaluate side-chains 232 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 199 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain Y residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 167 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 250 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 302 optimal weight: 7.9990 chunk 326 optimal weight: 0.3980 chunk 268 optimal weight: 0.1980 chunk 299 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 242 optimal weight: 7.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B1048 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 563 GLN C 969 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27662 Z= 0.175 Angle : 0.550 8.928 37614 Z= 0.275 Chirality : 0.045 0.275 4439 Planarity : 0.003 0.045 4765 Dihedral : 9.440 89.693 5000 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.52 % Allowed : 9.03 % Favored : 89.45 % 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: 0.33 (0.14), residues: 3288 helix: 1.77 (0.21), residues: 676 sheet: 0.29 (0.16), residues: 811 loop : -0.37 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 36 HIS 0.003 0.001 HIS C 519 PHE 0.026 0.001 PHE C 168 TYR 0.027 0.001 TYR A 200 ARG 0.004 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6308 (m-80) cc_final: 0.6090 (m-80) REVERT: A 190 ARG cc_start: 0.7098 (mtt90) cc_final: 0.6431 (mtp180) REVERT: A 278 LYS cc_start: 0.7365 (tttt) cc_final: 0.7093 (ttpp) REVERT: A 281 GLU cc_start: 0.7651 (tt0) cc_final: 0.7218 (pm20) REVERT: A 298 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6605 (mm-30) REVERT: A 591 SER cc_start: 0.8497 (t) cc_final: 0.8011 (p) REVERT: A 646 ARG cc_start: 0.7824 (mtp-110) cc_final: 0.7371 (mtt180) REVERT: A 654 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6581 (tt0) REVERT: A 869 MET cc_start: 0.7657 (mtt) cc_final: 0.7407 (mtp) REVERT: A 1050 MET cc_start: 0.8059 (ptt) cc_final: 0.7718 (ptm) REVERT: A 1101 HIS cc_start: 0.6805 (m90) cc_final: 0.6314 (m170) REVERT: A 1119 ASN cc_start: 0.7396 (m-40) cc_final: 0.7145 (m-40) REVERT: B 52 GLN cc_start: 0.7772 (tt0) cc_final: 0.6788 (pp30) REVERT: B 287 ASP cc_start: 0.7695 (t0) cc_final: 0.7229 (m-30) REVERT: B 360 ASN cc_start: 0.7636 (t0) cc_final: 0.7224 (m-40) REVERT: B 415 THR cc_start: 0.6202 (p) cc_final: 0.6001 (t) REVERT: B 510 VAL cc_start: 0.6965 (t) cc_final: 0.6754 (t) REVERT: B 605 SER cc_start: 0.9175 (t) cc_final: 0.8950 (t) REVERT: B 614 ASP cc_start: 0.7431 (p0) cc_final: 0.6687 (m-30) REVERT: B 646 ARG cc_start: 0.7988 (ttt90) cc_final: 0.7467 (mtt180) REVERT: B 661 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7779 (mt-10) REVERT: B 740 MET cc_start: 0.7731 (ttt) cc_final: 0.7221 (mtp) REVERT: B 755 GLN cc_start: 0.6800 (mt0) cc_final: 0.6450 (mm110) REVERT: B 994 ASP cc_start: 0.7082 (t70) cc_final: 0.6411 (m-30) REVERT: B 1045 LYS cc_start: 0.7922 (mmmt) cc_final: 0.7351 (mptt) REVERT: B 1050 MET cc_start: 0.8586 (ptt) cc_final: 0.8368 (ptm) REVERT: B 1092 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7445 (pp20) REVERT: C 47 VAL cc_start: 0.8048 (p) cc_final: 0.7807 (m) REVERT: C 97 LYS cc_start: 0.5381 (OUTLIER) cc_final: 0.5051 (ttpt) REVERT: C 138 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6685 (t0) REVERT: C 309 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6727 (mp0) REVERT: C 357 ARG cc_start: 0.7181 (ttt180) cc_final: 0.6883 (ttp-110) REVERT: C 529 LYS cc_start: 0.6581 (tptp) cc_final: 0.5995 (mtmt) REVERT: C 532 ASN cc_start: 0.7316 (t0) cc_final: 0.6856 (p0) REVERT: C 646 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7506 (ttt-90) REVERT: C 1045 LYS cc_start: 0.8608 (mtpp) cc_final: 0.8138 (mptt) REVERT: X 12 MET cc_start: 0.2086 (tpp) cc_final: 0.1770 (tpp) REVERT: X 34 MET cc_start: 0.3008 (mmm) cc_final: 0.2645 (ptt) REVERT: Y 83 MET cc_start: 0.3732 (mtp) cc_final: 0.3515 (mtm) outliers start: 44 outliers final: 33 residues processed: 266 average time/residue: 0.3900 time to fit residues: 165.6761 Evaluate side-chains 243 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain Y residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 298 optimal weight: 0.9990 chunk 227 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 320 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 87 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B1002 GLN B1135 ASN C 115 GLN C 394 ASN C 450 ASN C 474 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 914 ASN C 926 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 27662 Z= 0.385 Angle : 0.668 13.960 37614 Z= 0.337 Chirality : 0.049 0.269 4439 Planarity : 0.004 0.093 4765 Dihedral : 8.549 76.483 4994 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.52 % Allowed : 9.69 % Favored : 87.79 % 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: 0.18 (0.14), residues: 3288 helix: 1.42 (0.20), residues: 669 sheet: 0.32 (0.17), residues: 793 loop : -0.42 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1102 HIS 0.006 0.002 HIS C 519 PHE 0.025 0.002 PHE B 565 TYR 0.021 0.002 TYR B 369 ARG 0.006 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 242 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7821 (m-80) cc_final: 0.7253 (m-10) REVERT: A 190 ARG cc_start: 0.7043 (mtt90) cc_final: 0.6276 (mtp180) REVERT: A 200 TYR cc_start: 0.2596 (p90) cc_final: 0.2316 (p90) REVERT: A 278 LYS cc_start: 0.7356 (tttt) cc_final: 0.7141 (ttpt) REVERT: A 316 SER cc_start: 0.8369 (t) cc_final: 0.7897 (p) REVERT: A 365 TYR cc_start: 0.5814 (m-80) cc_final: 0.5562 (m-80) REVERT: A 544 ASN cc_start: 0.7904 (m-40) cc_final: 0.7648 (m-40) REVERT: A 591 SER cc_start: 0.8590 (t) cc_final: 0.8132 (p) REVERT: A 646 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7649 (mtm180) REVERT: A 654 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6776 (tt0) REVERT: A 1050 MET cc_start: 0.8293 (ptt) cc_final: 0.7982 (ptm) REVERT: A 1073 LYS cc_start: 0.7162 (mttt) cc_final: 0.6737 (mtpt) REVERT: A 1101 HIS cc_start: 0.7142 (m90) cc_final: 0.6622 (m170) REVERT: B 287 ASP cc_start: 0.7922 (t0) cc_final: 0.7289 (m-30) REVERT: B 360 ASN cc_start: 0.7680 (t0) cc_final: 0.7167 (m-40) REVERT: B 394 ASN cc_start: 0.7083 (m-40) cc_final: 0.6827 (t0) REVERT: B 589 PRO cc_start: 0.7399 (Cg_exo) cc_final: 0.6916 (Cg_endo) REVERT: B 614 ASP cc_start: 0.7536 (p0) cc_final: 0.6955 (m-30) REVERT: B 646 ARG cc_start: 0.8217 (ttt90) cc_final: 0.7558 (mtt180) REVERT: B 658 ASN cc_start: 0.5468 (t0) cc_final: 0.4949 (t0) REVERT: B 661 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7487 (tt0) REVERT: B 740 MET cc_start: 0.7895 (ttt) cc_final: 0.7391 (mtp) REVERT: B 1045 LYS cc_start: 0.7922 (mmmt) cc_final: 0.7317 (mmtm) REVERT: B 1050 MET cc_start: 0.8496 (ptt) cc_final: 0.8140 (ptm) REVERT: B 1092 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7575 (pp20) REVERT: C 97 LYS cc_start: 0.5540 (OUTLIER) cc_final: 0.5276 (ttpt) REVERT: C 138 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.6938 (t0) REVERT: C 309 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6791 (mp0) REVERT: C 355 ARG cc_start: 0.6407 (ttt180) cc_final: 0.5785 (ttm-80) REVERT: C 357 ARG cc_start: 0.7137 (ttt180) cc_final: 0.6684 (ttp80) REVERT: C 394 ASN cc_start: 0.6474 (OUTLIER) cc_final: 0.5916 (t0) REVERT: C 529 LYS cc_start: 0.6329 (tptp) cc_final: 0.5739 (mtmt) REVERT: C 532 ASN cc_start: 0.7390 (t0) cc_final: 0.6912 (p0) REVERT: C 537 LYS cc_start: 0.6293 (mttt) cc_final: 0.6020 (mtpt) REVERT: C 578 ASP cc_start: 0.8037 (t0) cc_final: 0.7819 (t0) REVERT: C 646 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7607 (ttt180) REVERT: C 1045 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8154 (mptt) REVERT: X 34 MET cc_start: 0.3729 (mmm) cc_final: 0.2648 (ptt) REVERT: Y 83 MET cc_start: 0.3846 (mtp) cc_final: 0.3635 (mtm) outliers start: 73 outliers final: 47 residues processed: 304 average time/residue: 0.3877 time to fit residues: 187.9300 Evaluate side-chains 259 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 209 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain Y residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 267 optimal weight: 0.7980 chunk 182 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 238 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 273 optimal weight: 0.6980 chunk 221 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 163 optimal weight: 0.9980 chunk 288 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 239 GLN B 388 ASN B1002 GLN C 239 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 27662 Z= 0.179 Angle : 0.549 9.894 37614 Z= 0.274 Chirality : 0.045 0.268 4439 Planarity : 0.003 0.044 4765 Dihedral : 7.674 71.321 4994 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.97 % Allowed : 11.31 % Favored : 86.72 % 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: 0.43 (0.14), residues: 3288 helix: 1.78 (0.21), residues: 661 sheet: 0.53 (0.17), residues: 783 loop : -0.34 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS C 519 PHE 0.017 0.001 PHE B 541 TYR 0.018 0.001 TYR A 369 ARG 0.004 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 214 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7464 (m-80) cc_final: 0.6811 (m-10) REVERT: A 190 ARG cc_start: 0.7025 (mtt90) cc_final: 0.6260 (mtp180) REVERT: A 278 LYS cc_start: 0.7439 (tttt) cc_final: 0.7158 (ttpt) REVERT: A 365 TYR cc_start: 0.5852 (m-80) cc_final: 0.5602 (m-10) REVERT: A 395 VAL cc_start: 0.4935 (t) cc_final: 0.4701 (t) REVERT: A 544 ASN cc_start: 0.7850 (m-40) cc_final: 0.7640 (m-40) REVERT: A 591 SER cc_start: 0.8560 (t) cc_final: 0.8115 (p) REVERT: A 646 ARG cc_start: 0.8039 (mtp-110) cc_final: 0.7617 (mtm180) REVERT: A 654 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6658 (tt0) REVERT: A 1050 MET cc_start: 0.8316 (ptt) cc_final: 0.8046 (ptm) REVERT: A 1072 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8325 (pm20) REVERT: A 1073 LYS cc_start: 0.7182 (mttt) cc_final: 0.6762 (mtpt) REVERT: A 1101 HIS cc_start: 0.7233 (m90) cc_final: 0.6803 (m170) REVERT: B 287 ASP cc_start: 0.7910 (t0) cc_final: 0.7250 (m-30) REVERT: B 332 ILE cc_start: 0.5967 (mt) cc_final: 0.5653 (pt) REVERT: B 360 ASN cc_start: 0.7666 (t0) cc_final: 0.7064 (m-40) REVERT: B 589 PRO cc_start: 0.7371 (Cg_exo) cc_final: 0.6916 (Cg_endo) REVERT: B 614 ASP cc_start: 0.7531 (p0) cc_final: 0.6853 (m-30) REVERT: B 646 ARG cc_start: 0.8243 (ttt90) cc_final: 0.7579 (mtt180) REVERT: B 661 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7303 (tt0) REVERT: B 675 GLN cc_start: 0.6535 (tt0) cc_final: 0.6207 (tm-30) REVERT: B 740 MET cc_start: 0.7591 (ttt) cc_final: 0.7141 (mtp) REVERT: B 1045 LYS cc_start: 0.7956 (mmmt) cc_final: 0.7417 (mptt) REVERT: B 1050 MET cc_start: 0.8412 (ptt) cc_final: 0.8129 (ptm) REVERT: B 1092 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7572 (pp20) REVERT: C 97 LYS cc_start: 0.5517 (OUTLIER) cc_final: 0.5269 (ttpt) REVERT: C 138 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7051 (t0) REVERT: C 355 ARG cc_start: 0.6336 (ttt180) cc_final: 0.5660 (ttm170) REVERT: C 357 ARG cc_start: 0.7232 (ttt180) cc_final: 0.7032 (ttp-110) REVERT: C 529 LYS cc_start: 0.6374 (tptp) cc_final: 0.5782 (mtmt) REVERT: C 532 ASN cc_start: 0.7550 (t0) cc_final: 0.6931 (p0) REVERT: C 537 LYS cc_start: 0.6273 (mttt) cc_final: 0.6034 (mtpt) REVERT: C 578 ASP cc_start: 0.7905 (t0) cc_final: 0.7667 (t0) REVERT: C 646 ARG cc_start: 0.7909 (tpp80) cc_final: 0.7618 (ttt180) REVERT: C 1045 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8134 (mptt) REVERT: C 1092 GLU cc_start: 0.8712 (tp30) cc_final: 0.7907 (pt0) REVERT: X 34 MET cc_start: 0.3509 (mmm) cc_final: 0.2673 (ptt) outliers start: 57 outliers final: 39 residues processed: 258 average time/residue: 0.3697 time to fit residues: 154.7536 Evaluate side-chains 241 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 199 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain Y residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 107 optimal weight: 1.9990 chunk 288 optimal weight: 0.0980 chunk 63 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 321 optimal weight: 30.0000 chunk 266 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 168 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1106 GLN C 81 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 27662 Z= 0.151 Angle : 0.516 8.302 37614 Z= 0.256 Chirality : 0.044 0.248 4439 Planarity : 0.003 0.039 4765 Dihedral : 6.848 63.369 4994 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.97 % Allowed : 11.66 % Favored : 86.38 % 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: 0.58 (0.14), residues: 3288 helix: 1.91 (0.21), residues: 668 sheet: 0.62 (0.17), residues: 772 loop : -0.25 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS C 519 PHE 0.026 0.001 PHE C 168 TYR 0.020 0.001 TYR A 200 ARG 0.007 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 204 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6982 (mtt90) cc_final: 0.6208 (mtp180) REVERT: A 278 LYS cc_start: 0.7479 (tttt) cc_final: 0.7259 (ttpt) REVERT: A 326 ILE cc_start: 0.7081 (mt) cc_final: 0.6862 (tt) REVERT: A 591 SER cc_start: 0.8571 (t) cc_final: 0.8037 (p) REVERT: A 646 ARG cc_start: 0.8019 (mtp-110) cc_final: 0.7575 (mtm180) REVERT: A 654 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6643 (tt0) REVERT: A 916 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6741 (tp) REVERT: A 1050 MET cc_start: 0.8199 (ptt) cc_final: 0.7978 (ptm) REVERT: A 1101 HIS cc_start: 0.7235 (m90) cc_final: 0.6789 (m170) REVERT: B 86 PHE cc_start: 0.4492 (t80) cc_final: 0.4172 (t80) REVERT: B 287 ASP cc_start: 0.7915 (t0) cc_final: 0.7263 (m-30) REVERT: B 332 ILE cc_start: 0.5966 (mt) cc_final: 0.5740 (pt) REVERT: B 360 ASN cc_start: 0.7566 (t0) cc_final: 0.6978 (m-40) REVERT: B 589 PRO cc_start: 0.7422 (Cg_exo) cc_final: 0.7033 (Cg_endo) REVERT: B 646 ARG cc_start: 0.8112 (ttt90) cc_final: 0.7479 (mpt-90) REVERT: B 661 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7257 (tt0) REVERT: B 675 GLN cc_start: 0.6580 (tt0) cc_final: 0.6259 (tm-30) REVERT: B 740 MET cc_start: 0.7572 (ttt) cc_final: 0.7159 (mtp) REVERT: B 1045 LYS cc_start: 0.7995 (mmmt) cc_final: 0.7478 (mptt) REVERT: B 1050 MET cc_start: 0.8300 (ptt) cc_final: 0.8074 (ptm) REVERT: B 1092 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7572 (pp20) REVERT: C 47 VAL cc_start: 0.7967 (p) cc_final: 0.7728 (m) REVERT: C 97 LYS cc_start: 0.5510 (OUTLIER) cc_final: 0.5241 (ttpt) REVERT: C 138 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.6802 (t0) REVERT: C 355 ARG cc_start: 0.6326 (ttt180) cc_final: 0.5824 (ttm-80) REVERT: C 357 ARG cc_start: 0.7185 (ttt180) cc_final: 0.6950 (ttp-110) REVERT: C 532 ASN cc_start: 0.7658 (t0) cc_final: 0.6898 (p0) REVERT: C 537 LYS cc_start: 0.6274 (mttt) cc_final: 0.6017 (mtpt) REVERT: C 578 ASP cc_start: 0.7914 (t0) cc_final: 0.7623 (t0) REVERT: C 646 ARG cc_start: 0.7936 (tpp80) cc_final: 0.7640 (ttt180) REVERT: C 1045 LYS cc_start: 0.8507 (mtpp) cc_final: 0.8093 (mptt) REVERT: C 1092 GLU cc_start: 0.8791 (tp30) cc_final: 0.7904 (pt0) REVERT: X 34 MET cc_start: 0.3382 (mmm) cc_final: 0.2537 (ptt) REVERT: Y 83 MET cc_start: 0.3774 (mtm) cc_final: 0.2653 (tmm) outliers start: 57 outliers final: 41 residues processed: 250 average time/residue: 0.3631 time to fit residues: 148.4484 Evaluate side-chains 231 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 187 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 309 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 319 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 239 GLN B1002 GLN C 81 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Y 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 27662 Z= 0.313 Angle : 0.602 10.049 37614 Z= 0.302 Chirality : 0.047 0.244 4439 Planarity : 0.004 0.039 4765 Dihedral : 6.756 57.110 4993 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.28 % Allowed : 11.59 % Favored : 86.14 % 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: 0.35 (0.14), residues: 3288 helix: 1.57 (0.20), residues: 672 sheet: 0.58 (0.17), residues: 795 loop : -0.40 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS C1048 PHE 0.020 0.002 PHE B 565 TYR 0.018 0.002 TYR A 369 ARG 0.005 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 219 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7107 (mtt90) cc_final: 0.6363 (mtp180) REVERT: A 278 LYS cc_start: 0.7398 (tttt) cc_final: 0.7186 (ttpt) REVERT: A 316 SER cc_start: 0.8397 (t) cc_final: 0.7933 (p) REVERT: A 326 ILE cc_start: 0.7075 (mt) cc_final: 0.6832 (tt) REVERT: A 591 SER cc_start: 0.8468 (t) cc_final: 0.7990 (p) REVERT: A 646 ARG cc_start: 0.8082 (mtp180) cc_final: 0.7679 (mtm180) REVERT: A 654 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6753 (tt0) REVERT: A 902 MET cc_start: 0.8054 (tpt) cc_final: 0.7497 (tpt) REVERT: A 1072 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8453 (pm20) REVERT: A 1073 LYS cc_start: 0.7231 (mttt) cc_final: 0.6754 (tttm) REVERT: A 1101 HIS cc_start: 0.7352 (m90) cc_final: 0.6964 (m170) REVERT: B 191 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7979 (mt-10) REVERT: B 287 ASP cc_start: 0.7910 (t0) cc_final: 0.7279 (m-30) REVERT: B 332 ILE cc_start: 0.5996 (mt) cc_final: 0.5709 (pt) REVERT: B 360 ASN cc_start: 0.7599 (t0) cc_final: 0.7012 (m-40) REVERT: B 495 TYR cc_start: 0.6807 (m-80) cc_final: 0.6570 (m-10) REVERT: B 589 PRO cc_start: 0.7601 (Cg_exo) cc_final: 0.7304 (Cg_endo) REVERT: B 646 ARG cc_start: 0.8233 (ttt90) cc_final: 0.7609 (mtm-85) REVERT: B 658 ASN cc_start: 0.5838 (t0) cc_final: 0.5233 (t0) REVERT: B 661 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7330 (tt0) REVERT: B 675 GLN cc_start: 0.6551 (tt0) cc_final: 0.6282 (tm-30) REVERT: B 740 MET cc_start: 0.7796 (ttt) cc_final: 0.7395 (mtp) REVERT: B 1045 LYS cc_start: 0.7790 (mmmt) cc_final: 0.7349 (mptt) REVERT: B 1050 MET cc_start: 0.8492 (ptt) cc_final: 0.8147 (ptm) REVERT: C 97 LYS cc_start: 0.5458 (OUTLIER) cc_final: 0.5180 (ttpt) REVERT: C 138 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.6749 (t0) REVERT: C 309 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6819 (mp0) REVERT: C 355 ARG cc_start: 0.6289 (ttt180) cc_final: 0.5850 (ttm-80) REVERT: C 357 ARG cc_start: 0.7223 (ttt180) cc_final: 0.6985 (ttp-110) REVERT: C 532 ASN cc_start: 0.7522 (t0) cc_final: 0.6782 (p0) REVERT: C 537 LYS cc_start: 0.6703 (mttt) cc_final: 0.6405 (mtpt) REVERT: C 578 ASP cc_start: 0.7881 (t0) cc_final: 0.7578 (t0) REVERT: C 646 ARG cc_start: 0.7910 (tpp80) cc_final: 0.7611 (ttt180) REVERT: C 1045 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8104 (mptt) REVERT: C 1101 HIS cc_start: 0.7014 (m90) cc_final: 0.6178 (m-70) REVERT: X 34 MET cc_start: 0.3724 (mmm) cc_final: 0.2699 (ptt) REVERT: Y 83 MET cc_start: 0.3521 (mtm) cc_final: 0.2364 (tmm) outliers start: 66 outliers final: 50 residues processed: 274 average time/residue: 0.3699 time to fit residues: 164.8049 Evaluate side-chains 261 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 208 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 10.0000 chunk 127 optimal weight: 0.0570 chunk 191 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 chunk 218 optimal weight: 0.0570 chunk 158 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 251 optimal weight: 0.9980 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 271 GLN B 613 GLN B1002 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 27662 Z= 0.149 Angle : 0.514 8.694 37614 Z= 0.256 Chirality : 0.044 0.242 4439 Planarity : 0.003 0.038 4765 Dihedral : 6.180 52.305 4993 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.62 % Allowed : 12.66 % Favored : 85.72 % 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: 0.60 (0.14), residues: 3288 helix: 1.94 (0.21), residues: 674 sheet: 0.64 (0.17), residues: 804 loop : -0.28 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS C 519 PHE 0.027 0.001 PHE A 392 TYR 0.018 0.001 TYR A 200 ARG 0.006 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 217 time to evaluate : 3.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7026 (mtt90) cc_final: 0.6318 (mtp180) REVERT: A 278 LYS cc_start: 0.7430 (tttt) cc_final: 0.7125 (ttpt) REVERT: A 326 ILE cc_start: 0.7101 (mt) cc_final: 0.6838 (tt) REVERT: A 591 SER cc_start: 0.8575 (t) cc_final: 0.7945 (p) REVERT: A 646 ARG cc_start: 0.8009 (mtp180) cc_final: 0.7620 (mtm180) REVERT: A 654 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6650 (tt0) REVERT: A 1073 LYS cc_start: 0.7222 (mttt) cc_final: 0.6867 (mtpp) REVERT: A 1101 HIS cc_start: 0.7251 (m90) cc_final: 0.6867 (m170) REVERT: B 287 ASP cc_start: 0.7902 (t0) cc_final: 0.7262 (m-30) REVERT: B 360 ASN cc_start: 0.7726 (t0) cc_final: 0.7062 (m-40) REVERT: B 589 PRO cc_start: 0.7589 (Cg_exo) cc_final: 0.7325 (Cg_endo) REVERT: B 646 ARG cc_start: 0.8249 (ttt90) cc_final: 0.7617 (mtm-85) REVERT: B 661 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7244 (tt0) REVERT: B 675 GLN cc_start: 0.6524 (tt0) cc_final: 0.6202 (tm-30) REVERT: B 740 MET cc_start: 0.7698 (ttt) cc_final: 0.7302 (mtp) REVERT: B 1045 LYS cc_start: 0.7851 (mmmt) cc_final: 0.7384 (mptt) REVERT: B 1050 MET cc_start: 0.8308 (ptt) cc_final: 0.8069 (ptm) REVERT: C 47 VAL cc_start: 0.7953 (p) cc_final: 0.7731 (m) REVERT: C 97 LYS cc_start: 0.5494 (OUTLIER) cc_final: 0.5213 (ttpt) REVERT: C 138 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6689 (t0) REVERT: C 355 ARG cc_start: 0.6326 (ttt180) cc_final: 0.5960 (ttm-80) REVERT: C 357 ARG cc_start: 0.7160 (ttt180) cc_final: 0.6875 (ttp80) REVERT: C 442 ASP cc_start: 0.3914 (m-30) cc_final: 0.3542 (m-30) REVERT: C 532 ASN cc_start: 0.7631 (t0) cc_final: 0.6898 (p0) REVERT: C 537 LYS cc_start: 0.6816 (mttt) cc_final: 0.6555 (mtpt) REVERT: C 578 ASP cc_start: 0.7994 (t0) cc_final: 0.7688 (t0) REVERT: C 646 ARG cc_start: 0.7842 (tpp80) cc_final: 0.7463 (ttt-90) REVERT: C 1045 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8083 (mptt) REVERT: X 34 MET cc_start: 0.3458 (mmm) cc_final: 0.2530 (ptt) REVERT: Y 83 MET cc_start: 0.3479 (mtm) cc_final: 0.2469 (tmm) outliers start: 47 outliers final: 37 residues processed: 256 average time/residue: 0.3803 time to fit residues: 158.3101 Evaluate side-chains 237 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 291 optimal weight: 0.9990 chunk 306 optimal weight: 4.9990 chunk 279 optimal weight: 0.6980 chunk 298 optimal weight: 0.2980 chunk 179 optimal weight: 2.9990 chunk 129 optimal weight: 0.0070 chunk 234 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 282 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 644 GLN B1002 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27662 Z= 0.174 Angle : 0.520 8.902 37614 Z= 0.259 Chirality : 0.044 0.252 4439 Planarity : 0.003 0.038 4765 Dihedral : 5.891 52.229 4993 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.52 % Allowed : 12.93 % Favored : 85.55 % 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: 0.62 (0.14), residues: 3288 helix: 1.94 (0.21), residues: 675 sheet: 0.69 (0.17), residues: 823 loop : -0.29 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS C 519 PHE 0.020 0.001 PHE B 86 TYR 0.019 0.001 TYR A 200 ARG 0.004 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 202 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7020 (mtt90) cc_final: 0.6303 (mtp180) REVERT: A 278 LYS cc_start: 0.7462 (tttt) cc_final: 0.7143 (ttpt) REVERT: A 316 SER cc_start: 0.8211 (t) cc_final: 0.7822 (p) REVERT: A 326 ILE cc_start: 0.7107 (mt) cc_final: 0.6887 (tt) REVERT: A 646 ARG cc_start: 0.8067 (mtp180) cc_final: 0.7659 (mtm180) REVERT: A 654 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6666 (tt0) REVERT: A 902 MET cc_start: 0.7943 (tpt) cc_final: 0.7502 (tpt) REVERT: A 1073 LYS cc_start: 0.7229 (mttt) cc_final: 0.6874 (mtpp) REVERT: A 1101 HIS cc_start: 0.7288 (m90) cc_final: 0.6911 (m170) REVERT: B 287 ASP cc_start: 0.8016 (t0) cc_final: 0.7422 (m-30) REVERT: B 358 ILE cc_start: 0.7336 (mm) cc_final: 0.7085 (mt) REVERT: B 360 ASN cc_start: 0.7670 (t0) cc_final: 0.7064 (m-40) REVERT: B 646 ARG cc_start: 0.8281 (ttt90) cc_final: 0.7660 (mtm-85) REVERT: B 661 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7311 (tt0) REVERT: B 675 GLN cc_start: 0.6513 (tt0) cc_final: 0.6195 (tm-30) REVERT: B 740 MET cc_start: 0.7818 (ttt) cc_final: 0.7427 (mtp) REVERT: B 1045 LYS cc_start: 0.7853 (mmmt) cc_final: 0.7401 (mptt) REVERT: B 1050 MET cc_start: 0.8438 (ptt) cc_final: 0.8181 (ptm) REVERT: C 47 VAL cc_start: 0.7979 (p) cc_final: 0.7764 (m) REVERT: C 97 LYS cc_start: 0.5499 (OUTLIER) cc_final: 0.5222 (ttpt) REVERT: C 138 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.7102 (p0) REVERT: C 357 ARG cc_start: 0.7470 (ttt180) cc_final: 0.7031 (ttp80) REVERT: C 442 ASP cc_start: 0.4289 (m-30) cc_final: 0.3842 (m-30) REVERT: C 532 ASN cc_start: 0.7620 (t0) cc_final: 0.6878 (p0) REVERT: C 537 LYS cc_start: 0.6933 (mttt) cc_final: 0.6665 (mtpt) REVERT: C 578 ASP cc_start: 0.7946 (t0) cc_final: 0.7621 (t0) REVERT: C 646 ARG cc_start: 0.7843 (tpp80) cc_final: 0.7470 (ttt-90) REVERT: C 796 ASP cc_start: 0.7901 (p0) cc_final: 0.7160 (t0) REVERT: C 1045 LYS cc_start: 0.8524 (mtpp) cc_final: 0.8126 (mptt) REVERT: X 34 MET cc_start: 0.3494 (mmm) cc_final: 0.2529 (ptt) REVERT: Y 83 MET cc_start: 0.3475 (mtm) cc_final: 0.2434 (tmm) outliers start: 44 outliers final: 37 residues processed: 236 average time/residue: 0.3851 time to fit residues: 146.8598 Evaluate side-chains 234 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 195 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 195 optimal weight: 1.9990 chunk 315 optimal weight: 20.0000 chunk 192 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 330 optimal weight: 6.9990 chunk 304 optimal weight: 8.9990 chunk 263 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 388 ASN B 613 GLN B1002 GLN C 388 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 27662 Z= 0.301 Angle : 0.586 10.899 37614 Z= 0.292 Chirality : 0.046 0.257 4439 Planarity : 0.004 0.052 4765 Dihedral : 6.153 56.661 4993 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.66 % Allowed : 13.00 % Favored : 85.34 % 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: 0.41 (0.14), residues: 3288 helix: 1.68 (0.21), residues: 678 sheet: 0.58 (0.17), residues: 822 loop : -0.39 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS C 519 PHE 0.017 0.002 PHE B 86 TYR 0.032 0.001 TYR A 423 ARG 0.004 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 192 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7004 (mtt90) cc_final: 0.6357 (mtp180) REVERT: A 278 LYS cc_start: 0.7401 (tttt) cc_final: 0.7133 (ttpt) REVERT: A 316 SER cc_start: 0.8341 (t) cc_final: 0.7924 (p) REVERT: A 326 ILE cc_start: 0.7090 (mt) cc_final: 0.6852 (tt) REVERT: A 537 LYS cc_start: 0.6963 (mttp) cc_final: 0.6602 (mtpt) REVERT: A 646 ARG cc_start: 0.8056 (mtp180) cc_final: 0.7660 (mtm180) REVERT: A 654 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6708 (tt0) REVERT: A 1073 LYS cc_start: 0.7132 (mttt) cc_final: 0.6788 (mtpp) REVERT: A 1101 HIS cc_start: 0.7367 (m90) cc_final: 0.7165 (m-70) REVERT: B 117 LEU cc_start: 0.5730 (mp) cc_final: 0.5412 (tp) REVERT: B 187 LYS cc_start: 0.6710 (mttt) cc_final: 0.6399 (mmmt) REVERT: B 287 ASP cc_start: 0.7977 (t0) cc_final: 0.7406 (m-30) REVERT: B 358 ILE cc_start: 0.7361 (mm) cc_final: 0.7043 (mt) REVERT: B 360 ASN cc_start: 0.7724 (t0) cc_final: 0.6989 (m110) REVERT: B 646 ARG cc_start: 0.8224 (ttt90) cc_final: 0.7597 (mtm-85) REVERT: B 658 ASN cc_start: 0.5938 (t0) cc_final: 0.5318 (t0) REVERT: B 661 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7349 (tt0) REVERT: B 675 GLN cc_start: 0.6531 (tt0) cc_final: 0.6216 (tm-30) REVERT: B 740 MET cc_start: 0.7856 (ttt) cc_final: 0.7430 (mtp) REVERT: B 1045 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7359 (mptt) REVERT: B 1050 MET cc_start: 0.8501 (ptt) cc_final: 0.8136 (ptm) REVERT: C 97 LYS cc_start: 0.5523 (OUTLIER) cc_final: 0.5234 (ttpt) REVERT: C 138 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.7021 (p0) REVERT: C 309 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6824 (mp0) REVERT: C 357 ARG cc_start: 0.7427 (ttt180) cc_final: 0.7050 (ttp80) REVERT: C 442 ASP cc_start: 0.4262 (m-30) cc_final: 0.3981 (t0) REVERT: C 532 ASN cc_start: 0.7557 (t0) cc_final: 0.6861 (p0) REVERT: C 537 LYS cc_start: 0.6927 (mttt) cc_final: 0.6690 (mtpt) REVERT: C 578 ASP cc_start: 0.7926 (t0) cc_final: 0.7597 (t0) REVERT: C 646 ARG cc_start: 0.7810 (tpp80) cc_final: 0.7500 (ttt180) REVERT: C 1045 LYS cc_start: 0.8564 (mtpp) cc_final: 0.8156 (mptt) REVERT: X 34 MET cc_start: 0.3691 (mmm) cc_final: 0.2641 (ptt) REVERT: Y 83 MET cc_start: 0.3441 (mtm) cc_final: 0.2536 (tmm) outliers start: 48 outliers final: 43 residues processed: 232 average time/residue: 0.3832 time to fit residues: 144.8605 Evaluate side-chains 232 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 187 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 209 optimal weight: 0.7980 chunk 280 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 242 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 263 optimal weight: 0.0170 chunk 110 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B1002 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 926 GLN C1142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.196694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.161060 restraints weight = 32512.697| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.80 r_work: 0.3596 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 27662 Z= 0.159 Angle : 0.517 10.032 37614 Z= 0.257 Chirality : 0.044 0.259 4439 Planarity : 0.003 0.035 4765 Dihedral : 5.754 56.837 4993 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.55 % Allowed : 13.28 % Favored : 85.17 % 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: 0.60 (0.14), residues: 3288 helix: 1.87 (0.21), residues: 686 sheet: 0.68 (0.17), residues: 823 loop : -0.29 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.005 0.001 HIS C 519 PHE 0.018 0.001 PHE B 86 TYR 0.021 0.001 TYR A 200 ARG 0.004 0.000 ARG A 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5205.81 seconds wall clock time: 95 minutes 58.18 seconds (5758.18 seconds total)