Starting phenix.real_space_refine on Mon Feb 19 07:33:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwv_11497/02_2024/6zwv_11497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwv_11497/02_2024/6zwv_11497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwv_11497/02_2024/6zwv_11497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwv_11497/02_2024/6zwv_11497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwv_11497/02_2024/6zwv_11497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwv_11497/02_2024/6zwv_11497.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 99 5.16 5 C 15297 2.51 5 N 3909 2.21 5 O 4710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C GLU 1111": "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: 24015 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7711 Classifications: {'peptide': 985} Link IDs: {'PTRANS': 46, 'TRANS': 938} Chain breaks: 8 Chain: "B" Number of atoms: 7711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7711 Classifications: {'peptide': 985} Link IDs: {'PTRANS': 46, 'TRANS': 938} Chain breaks: 8 Chain: "C" Number of atoms: 7711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7711 Classifications: {'peptide': 985} Link IDs: {'PTRANS': 46, 'TRANS': 938} Chain breaks: 8 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: "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: "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: "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: "X" 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: "b" 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: "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: "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: "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: "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: "4" 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: "6" 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: "9" 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: "BA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 11.88, per 1000 atoms: 0.49 Number of scatterers: 24015 At special positions: 0 Unit cell: (130.503, 137.93, 180.37, 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 99 16.00 O 4710 8.00 N 3909 7.00 C 15297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 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=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 4 1 " - " NAG 4 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 9 1 " - " NAG 9 2 " " NAG F 1 " - " NAG F 2 " " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG V 1 " - " NAG V 2 " " NAG X 1 " - " NAG X 2 " " NAG b 1 " - " NAG b 2 " " NAG k 1 " - " NAG k 2 " " NAG m 1 " - " NAG m 2 " " NAG p 1 " - " NAG p 2 " " NAG r 1 " - " NAG r 2 " " NAG v 1 " - " NAG v 2 " " NAGBA 1 " - " NAGBA 2 " NAG-ASN " NAG 4 1 " - " ASN C 717 " " NAG 6 1 " - " ASN C 801 " " NAG 9 1 " - " ASN C1098 " " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 165 " " NAG F 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 717 " " NAG S 1 " - " ASN A 801 " " NAG V 1 " - " ASN A1098 " " NAG X 1 " - " ASN A1134 " " NAG b 1 " - " ASN B 234 " " NAG k 1 " - " ASN B 717 " " NAG m 1 " - " ASN B 801 " " NAG p 1 " - " ASN B1098 " " NAG r 1 " - " ASN B1134 " " NAG v 1 " - " ASN C 234 " " NAGBA 1 " - " ASN C1134 " Time building additional restraints: 8.92 Conformation dependent library (CDL) restraints added in 3.7 seconds 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 42 sheets defined 26.2% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.109A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.900A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.041A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.838A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.621A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.021A 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: 3.894A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.885A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.192A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1151 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.108A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.900A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 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 755 Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.041A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.838A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.623A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.020A 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: 3.894A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.885A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.192A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1151 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.109A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.900A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.041A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.838A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.622A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.020A 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: 3.894A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.884A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.193A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1151 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.915A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.164A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.363A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.586A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.040A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.324A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.164A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.823A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.523A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.523A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.094A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.826A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.555A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.915A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.164A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.363A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.586A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.041A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.325A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.823A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.523A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.523A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.095A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.713A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.555A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.915A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.362A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.585A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.236A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.325A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.823A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.523A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.523A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.095A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.555A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 931 hydrogen bonds defined for protein. 2628 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: 10.22 Time building geometry restraints manager: 9.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7591 1.35 - 1.48: 6585 1.48 - 1.60: 10226 1.60 - 1.73: 3 1.73 - 1.86: 123 Bond restraints: 24528 Sorted by residual: bond pdb=" CB GLN A 755 " pdb=" CG GLN A 755 " ideal model delta sigma weight residual 1.520 1.608 -0.088 3.00e-02 1.11e+03 8.51e+00 bond pdb=" CB GLN C 755 " pdb=" CG GLN C 755 " ideal model delta sigma weight residual 1.520 1.607 -0.087 3.00e-02 1.11e+03 8.49e+00 bond pdb=" CB GLN B 755 " pdb=" CG GLN B 755 " ideal model delta sigma weight residual 1.520 1.607 -0.087 3.00e-02 1.11e+03 8.37e+00 bond pdb=" CG1 ILE B 896 " pdb=" CD1 ILE B 896 " ideal model delta sigma weight residual 1.513 1.403 0.110 3.90e-02 6.57e+02 7.92e+00 bond pdb=" CG1 ILE C 896 " pdb=" CD1 ILE C 896 " ideal model delta sigma weight residual 1.513 1.403 0.110 3.90e-02 6.57e+02 7.92e+00 ... (remaining 24523 not shown) Histogram of bond angle deviations from ideal: 91.84 - 102.57: 75 102.57 - 113.31: 13927 113.31 - 124.05: 18739 124.05 - 134.79: 601 134.79 - 145.53: 9 Bond angle restraints: 33351 Sorted by residual: angle pdb=" CB ARG A 214 " pdb=" CG ARG A 214 " pdb=" CD ARG A 214 " ideal model delta sigma weight residual 111.30 142.58 -31.28 2.30e+00 1.89e-01 1.85e+02 angle pdb=" CB ARG C 214 " pdb=" CG ARG C 214 " pdb=" CD ARG C 214 " ideal model delta sigma weight residual 111.30 142.58 -31.28 2.30e+00 1.89e-01 1.85e+02 angle pdb=" CB ARG B 214 " pdb=" CG ARG B 214 " pdb=" CD ARG B 214 " ideal model delta sigma weight residual 111.30 142.56 -31.26 2.30e+00 1.89e-01 1.85e+02 angle pdb=" CG ARG A1107 " pdb=" CD ARG A1107 " pdb=" NE ARG A1107 " ideal model delta sigma weight residual 112.00 140.16 -28.16 2.20e+00 2.07e-01 1.64e+02 angle pdb=" CG ARG B1107 " pdb=" CD ARG B1107 " pdb=" NE ARG B1107 " ideal model delta sigma weight residual 112.00 140.07 -28.07 2.20e+00 2.07e-01 1.63e+02 ... (remaining 33346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 14461 24.09 - 48.19: 717 48.19 - 72.28: 176 72.28 - 96.37: 57 96.37 - 120.47: 9 Dihedral angle restraints: 15420 sinusoidal: 6822 harmonic: 8598 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 31.71 61.29 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 31.73 61.27 1 1.00e+01 1.00e-02 4.98e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 31.74 61.26 1 1.00e+01 1.00e-02 4.98e+01 ... (remaining 15417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.292: 3954 0.292 - 0.584: 15 0.584 - 0.877: 9 0.877 - 1.169: 3 1.169 - 1.461: 9 Chirality restraints: 3990 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -0.94 -1.46 2.00e-01 2.50e+01 5.33e+01 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -0.94 -1.46 2.00e-01 2.50e+01 5.33e+01 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -0.94 -1.46 2.00e-01 2.50e+01 5.33e+01 ... (remaining 3987 not shown) Planarity restraints: 4269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.086 2.00e-02 2.50e+03 7.55e-02 7.12e+01 pdb=" C7 NAG A1304 " -0.030 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " -0.013 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.119 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " -0.086 2.00e-02 2.50e+03 7.53e-02 7.09e+01 pdb=" C7 NAG B1304 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " 0.013 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " 0.119 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " -0.086 2.00e-02 2.50e+03 7.52e-02 7.07e+01 pdb=" C7 NAG C1304 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " 0.013 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " 0.118 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " -0.076 2.00e-02 2.50e+03 ... (remaining 4266 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 274 2.60 - 3.18: 21137 3.18 - 3.75: 35686 3.75 - 4.33: 51272 4.33 - 4.90: 83714 Nonbonded interactions: 192083 Sorted by model distance: nonbonded pdb=" OG1 THR A 716 " pdb=" O GLN A1071 " model vdw 2.025 2.440 nonbonded pdb=" OG1 THR B 716 " pdb=" O GLN B1071 " model vdw 2.025 2.440 nonbonded pdb=" OG1 THR C 716 " pdb=" O GLN C1071 " model vdw 2.026 2.440 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.068 2.440 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.068 2.440 ... (remaining 192078 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 '4' selection = chain '6' selection = chain '9' selection = chain 'BA' selection = chain 'F' selection = chain 'Q' selection = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'b' selection = chain 'k' selection = chain 'm' selection = chain 'p' selection = chain 'r' selection = chain 'v' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 4.840 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 61.500 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.010 0.110 24528 Z= 0.636 Angle : 1.354 32.832 33351 Z= 0.688 Chirality : 0.098 1.461 3990 Planarity : 0.008 0.132 4221 Dihedral : 16.195 120.466 9768 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.74 % Allowed : 0.89 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 2901 helix: 0.40 (0.19), residues: 663 sheet: -1.32 (0.20), residues: 600 loop : -1.75 (0.13), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.005 TRP C 104 HIS 0.008 0.002 HIS B 655 PHE 0.059 0.004 PHE B 464 TYR 0.079 0.003 TYR C 904 ARG 0.083 0.004 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 194 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8391 (m-90) cc_final: 0.8023 (m-90) REVERT: A 239 GLN cc_start: 0.8200 (mm110) cc_final: 0.7984 (mm-40) REVERT: A 389 ASP cc_start: 0.8927 (m-30) cc_final: 0.8506 (m-30) REVERT: A 516 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7453 (tp30) REVERT: A 517 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8173 (mm) REVERT: A 584 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8482 (tp) REVERT: A 978 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8155 (t0) REVERT: A 985 ASP cc_start: 0.8006 (m-30) cc_final: 0.7490 (m-30) REVERT: A 1107 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7784 (ttm110) REVERT: B 389 ASP cc_start: 0.8855 (m-30) cc_final: 0.8489 (m-30) REVERT: B 508 TYR cc_start: 0.7306 (m-80) cc_final: 0.6929 (m-80) REVERT: B 517 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8243 (mm) REVERT: B 584 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8538 (tp) REVERT: B 869 MET cc_start: 0.8189 (mtt) cc_final: 0.7920 (mtt) REVERT: B 1107 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7685 (ttm170) REVERT: C 389 ASP cc_start: 0.8849 (m-30) cc_final: 0.8399 (m-30) REVERT: C 584 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8606 (tp) REVERT: C 751 ASN cc_start: 0.8671 (m-40) cc_final: 0.8287 (m-40) REVERT: C 1107 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7913 (ttm170) outliers start: 45 outliers final: 11 residues processed: 220 average time/residue: 0.3396 time to fit residues: 120.4821 Evaluate side-chains 154 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 119 optimal weight: 0.7980 chunk 230 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 171 optimal weight: 0.3980 chunk 266 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 955 ASN A 957 GLN A1005 GLN A1113 GLN B 66 HIS B 955 ASN B1005 GLN C 66 HIS C 955 ASN C 957 GLN C1005 GLN C1113 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24528 Z= 0.186 Angle : 0.731 13.271 33351 Z= 0.356 Chirality : 0.067 0.941 3990 Planarity : 0.004 0.051 4221 Dihedral : 11.438 108.626 4530 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.31 % Allowed : 6.06 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 2901 helix: 1.19 (0.19), residues: 690 sheet: -1.00 (0.18), residues: 645 loop : -1.38 (0.14), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 436 HIS 0.002 0.001 HIS B 207 PHE 0.026 0.002 PHE A 92 TYR 0.015 0.001 TYR C 380 ARG 0.009 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 2.618 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 104 TRP cc_start: 0.8190 (m-90) cc_final: 0.7950 (m-90) REVERT: A 269 TYR cc_start: 0.8372 (m-80) cc_final: 0.7820 (m-10) REVERT: A 389 ASP cc_start: 0.8912 (m-30) cc_final: 0.8543 (m-30) REVERT: A 508 TYR cc_start: 0.7623 (m-80) cc_final: 0.7361 (m-80) REVERT: A 584 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8638 (tp) REVERT: A 768 THR cc_start: 0.9389 (m) cc_final: 0.9043 (p) REVERT: A 985 ASP cc_start: 0.7809 (m-30) cc_final: 0.7289 (m-30) REVERT: B 223 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8792 (tp) REVERT: B 269 TYR cc_start: 0.8431 (m-80) cc_final: 0.8179 (m-80) REVERT: B 389 ASP cc_start: 0.8895 (m-30) cc_final: 0.8557 (m-30) REVERT: B 508 TYR cc_start: 0.7500 (m-80) cc_final: 0.7233 (m-80) REVERT: C 269 TYR cc_start: 0.8499 (m-80) cc_final: 0.8017 (m-80) REVERT: C 389 ASP cc_start: 0.8820 (m-30) cc_final: 0.8398 (m-30) REVERT: C 985 ASP cc_start: 0.7741 (m-30) cc_final: 0.7172 (m-30) outliers start: 34 outliers final: 15 residues processed: 200 average time/residue: 0.3159 time to fit residues: 104.9918 Evaluate side-chains 155 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 759 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 222 optimal weight: 30.0000 chunk 181 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 267 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 chunk 238 optimal weight: 0.0050 chunk 265 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 755 GLN A 901 GLN A 919 ASN A 926 GLN A 978 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 926 GLN C 901 GLN C 926 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24528 Z= 0.216 Angle : 0.643 11.855 33351 Z= 0.312 Chirality : 0.060 0.839 3990 Planarity : 0.004 0.047 4221 Dihedral : 9.378 99.660 4478 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.24 % Allowed : 9.81 % Favored : 88.95 % 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: -0.63 (0.15), residues: 2901 helix: 1.45 (0.20), residues: 690 sheet: -0.74 (0.19), residues: 681 loop : -1.13 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 436 HIS 0.003 0.001 HIS C1064 PHE 0.018 0.002 PHE A 192 TYR 0.023 0.001 TYR C 380 ARG 0.008 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 2.816 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 104 TRP cc_start: 0.8542 (m-90) cc_final: 0.8288 (m-90) REVERT: A 584 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8732 (tp) REVERT: A 768 THR cc_start: 0.9434 (m) cc_final: 0.9090 (p) REVERT: A 960 ASN cc_start: 0.8182 (m-40) cc_final: 0.7848 (t0) REVERT: B 223 LEU cc_start: 0.8986 (mt) cc_final: 0.8765 (tp) REVERT: B 269 TYR cc_start: 0.8391 (m-80) cc_final: 0.7987 (m-10) REVERT: B 389 ASP cc_start: 0.8925 (m-30) cc_final: 0.8607 (m-30) REVERT: B 508 TYR cc_start: 0.7710 (m-80) cc_final: 0.7361 (m-80) REVERT: B 979 ASP cc_start: 0.8190 (t0) cc_final: 0.7750 (t0) REVERT: C 269 TYR cc_start: 0.8449 (m-80) cc_final: 0.7830 (m-80) REVERT: C 979 ASP cc_start: 0.8078 (t0) cc_final: 0.7724 (t0) outliers start: 32 outliers final: 14 residues processed: 188 average time/residue: 0.3287 time to fit residues: 100.9962 Evaluate side-chains 147 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 127 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 254 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24528 Z= 0.299 Angle : 0.640 9.639 33351 Z= 0.314 Chirality : 0.057 0.762 3990 Planarity : 0.004 0.070 4221 Dihedral : 8.969 97.871 4475 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.82 % Allowed : 11.78 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 2901 helix: 1.35 (0.20), residues: 693 sheet: -0.71 (0.18), residues: 654 loop : -0.91 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 436 HIS 0.005 0.001 HIS C1064 PHE 0.018 0.001 PHE C 906 TYR 0.018 0.001 TYR C 904 ARG 0.014 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 142 time to evaluate : 2.676 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 104 TRP cc_start: 0.8599 (m-90) cc_final: 0.8356 (m-90) REVERT: A 369 TYR cc_start: 0.8174 (t80) cc_final: 0.7848 (t80) REVERT: A 508 TYR cc_start: 0.8219 (m-80) cc_final: 0.7825 (m-80) REVERT: A 960 ASN cc_start: 0.8232 (m-40) cc_final: 0.7964 (t0) REVERT: B 52 GLN cc_start: 0.8861 (tt0) cc_final: 0.8254 (tm-30) REVERT: B 223 LEU cc_start: 0.9083 (mt) cc_final: 0.8813 (tp) REVERT: B 269 TYR cc_start: 0.8515 (m-80) cc_final: 0.8117 (m-10) REVERT: B 508 TYR cc_start: 0.8084 (m-80) cc_final: 0.7671 (m-80) REVERT: C 87 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.7765 (p0) REVERT: C 104 TRP cc_start: 0.8699 (m-90) cc_final: 0.8065 (m-90) REVERT: C 568 ASP cc_start: 0.8402 (t0) cc_final: 0.7736 (p0) REVERT: C 740 MET cc_start: 0.8830 (tpp) cc_final: 0.8590 (tpp) REVERT: C 985 ASP cc_start: 0.7553 (m-30) cc_final: 0.6859 (m-30) outliers start: 47 outliers final: 24 residues processed: 180 average time/residue: 0.3026 time to fit residues: 93.0493 Evaluate side-chains 151 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 211 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 242 optimal weight: 1.9990 chunk 196 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 chunk 255 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN B 394 ASN C 919 ASN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24528 Z= 0.353 Angle : 0.653 13.600 33351 Z= 0.317 Chirality : 0.056 0.698 3990 Planarity : 0.004 0.047 4221 Dihedral : 8.789 96.882 4473 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.89 % Allowed : 12.78 % Favored : 85.32 % 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: -0.39 (0.15), residues: 2901 helix: 1.20 (0.20), residues: 711 sheet: -0.60 (0.18), residues: 660 loop : -0.75 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.005 0.001 HIS C1058 PHE 0.018 0.001 PHE A 906 TYR 0.014 0.001 TYR C 904 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 126 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8787 (p) REVERT: A 104 TRP cc_start: 0.8704 (m-90) cc_final: 0.8464 (m-90) REVERT: A 369 TYR cc_start: 0.8092 (t80) cc_final: 0.7771 (t80) REVERT: A 512 VAL cc_start: 0.9448 (t) cc_final: 0.9211 (p) REVERT: A 759 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8226 (t80) REVERT: B 33 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8737 (p) REVERT: B 52 GLN cc_start: 0.8923 (tt0) cc_final: 0.8318 (tm-30) REVERT: B 269 TYR cc_start: 0.8586 (m-80) cc_final: 0.8208 (m-10) REVERT: B 508 TYR cc_start: 0.8344 (m-80) cc_final: 0.7917 (m-80) REVERT: B 759 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8397 (t80) REVERT: C 33 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8811 (p) REVERT: C 87 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.7810 (p0) REVERT: C 104 TRP cc_start: 0.8771 (m-90) cc_final: 0.8155 (m-90) REVERT: C 740 MET cc_start: 0.8859 (tpp) cc_final: 0.8620 (tpp) REVERT: C 985 ASP cc_start: 0.7520 (m-30) cc_final: 0.6819 (m-30) outliers start: 49 outliers final: 30 residues processed: 163 average time/residue: 0.3019 time to fit residues: 84.3777 Evaluate side-chains 150 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 856 ASN B 271 GLN B 856 ASN C 856 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24528 Z= 0.205 Angle : 0.585 11.031 33351 Z= 0.282 Chirality : 0.053 0.659 3990 Planarity : 0.003 0.048 4221 Dihedral : 8.517 95.525 4473 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.01 % Allowed : 13.44 % Favored : 84.55 % 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: -0.25 (0.15), residues: 2901 helix: 1.45 (0.20), residues: 708 sheet: -0.58 (0.19), residues: 636 loop : -0.71 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.002 0.001 HIS C1064 PHE 0.014 0.001 PHE A1148 TYR 0.012 0.001 TYR C 204 ARG 0.008 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 139 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8756 (p) REVERT: A 104 TRP cc_start: 0.8669 (m-90) cc_final: 0.8402 (m-90) REVERT: A 369 TYR cc_start: 0.8076 (t80) cc_final: 0.7790 (t80) REVERT: A 512 VAL cc_start: 0.9418 (t) cc_final: 0.9202 (p) REVERT: A 759 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8191 (t80) REVERT: A 960 ASN cc_start: 0.8262 (m-40) cc_final: 0.7978 (t0) REVERT: B 33 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8719 (p) REVERT: B 52 GLN cc_start: 0.8908 (tt0) cc_final: 0.8327 (tm-30) REVERT: B 239 GLN cc_start: 0.8225 (mm110) cc_final: 0.7890 (mm-40) REVERT: B 269 TYR cc_start: 0.8548 (m-80) cc_final: 0.8111 (m-10) REVERT: B 508 TYR cc_start: 0.8412 (m-80) cc_final: 0.7963 (m-80) REVERT: C 87 ASN cc_start: 0.8514 (m-40) cc_final: 0.7791 (p0) REVERT: C 104 TRP cc_start: 0.8691 (m-90) cc_final: 0.8189 (m-90) REVERT: C 369 TYR cc_start: 0.8380 (t80) cc_final: 0.8064 (t80) REVERT: C 740 MET cc_start: 0.8784 (tpp) cc_final: 0.8572 (tpp) REVERT: C 985 ASP cc_start: 0.7543 (m-30) cc_final: 0.6872 (m-30) outliers start: 52 outliers final: 36 residues processed: 180 average time/residue: 0.2830 time to fit residues: 88.7862 Evaluate side-chains 158 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 119 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 207 optimal weight: 30.0000 chunk 160 optimal weight: 0.6980 chunk 239 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 283 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 856 ASN B1005 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 394 ASN C 856 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 24528 Z= 0.300 Angle : 0.613 10.242 33351 Z= 0.298 Chirality : 0.053 0.621 3990 Planarity : 0.004 0.047 4221 Dihedral : 8.315 96.081 4473 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.09 % Allowed : 14.21 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 2901 helix: 1.44 (0.20), residues: 702 sheet: -0.50 (0.18), residues: 675 loop : -0.65 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 886 HIS 0.004 0.001 HIS C1064 PHE 0.026 0.001 PHE A 201 TYR 0.031 0.001 TYR B 904 ARG 0.005 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 127 time to evaluate : 2.682 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 33 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8808 (p) REVERT: A 104 TRP cc_start: 0.8704 (m-90) cc_final: 0.8369 (m-90) REVERT: A 369 TYR cc_start: 0.8200 (t80) cc_final: 0.7858 (t80) REVERT: A 759 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8140 (t80) REVERT: B 33 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8744 (p) REVERT: B 52 GLN cc_start: 0.8942 (tt0) cc_final: 0.8358 (tm-30) REVERT: B 269 TYR cc_start: 0.8593 (m-80) cc_final: 0.8198 (m-10) REVERT: B 508 TYR cc_start: 0.8556 (m-80) cc_final: 0.8134 (m-80) REVERT: C 33 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8797 (p) REVERT: C 87 ASN cc_start: 0.8532 (m-40) cc_final: 0.7767 (p0) REVERT: C 104 TRP cc_start: 0.8786 (m-90) cc_final: 0.8314 (m-90) outliers start: 54 outliers final: 42 residues processed: 168 average time/residue: 0.2784 time to fit residues: 82.3764 Evaluate side-chains 157 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 111 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 0.0170 chunk 113 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 222 optimal weight: 6.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN C 125 ASN C1106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24528 Z= 0.146 Angle : 0.560 10.144 33351 Z= 0.270 Chirality : 0.052 0.589 3990 Planarity : 0.003 0.048 4221 Dihedral : 7.937 94.492 4473 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.62 % Allowed : 15.06 % Favored : 83.31 % 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: 0.01 (0.15), residues: 2901 helix: 1.73 (0.20), residues: 702 sheet: -0.31 (0.19), residues: 633 loop : -0.62 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 104 HIS 0.001 0.000 HIS B1083 PHE 0.023 0.001 PHE A 201 TYR 0.042 0.001 TYR C 904 ARG 0.005 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 133 time to evaluate : 2.434 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 33 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8718 (p) REVERT: A 104 TRP cc_start: 0.8563 (m-90) cc_final: 0.8218 (m-90) REVERT: A 369 TYR cc_start: 0.8167 (t80) cc_final: 0.7873 (t80) REVERT: A 759 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8155 (t80) REVERT: A 960 ASN cc_start: 0.8297 (m-40) cc_final: 0.8091 (t0) REVERT: B 33 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8686 (p) REVERT: B 52 GLN cc_start: 0.8916 (tt0) cc_final: 0.8352 (tm-30) REVERT: B 269 TYR cc_start: 0.8506 (m-80) cc_final: 0.8086 (m-10) REVERT: B 354 ASN cc_start: 0.9168 (t0) cc_final: 0.8125 (p0) REVERT: B 508 TYR cc_start: 0.8592 (m-80) cc_final: 0.8165 (m-80) REVERT: B 740 MET cc_start: 0.8912 (tpp) cc_final: 0.8618 (tpp) REVERT: B 759 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8292 (t80) REVERT: C 33 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8789 (p) REVERT: C 52 GLN cc_start: 0.8916 (tt0) cc_final: 0.8506 (tm-30) REVERT: C 87 ASN cc_start: 0.8543 (m-40) cc_final: 0.7789 (p0) REVERT: C 104 TRP cc_start: 0.8758 (m-90) cc_final: 0.8384 (m-90) REVERT: C 354 ASN cc_start: 0.9248 (t0) cc_final: 0.8918 (t0) outliers start: 42 outliers final: 34 residues processed: 168 average time/residue: 0.2788 time to fit residues: 82.2242 Evaluate side-chains 164 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 4.9990 chunk 271 optimal weight: 0.8980 chunk 247 optimal weight: 7.9990 chunk 264 optimal weight: 9.9990 chunk 158 optimal weight: 0.4980 chunk 115 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 238 optimal weight: 0.8980 chunk 249 optimal weight: 0.8980 chunk 263 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN C 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24528 Z= 0.145 Angle : 0.547 9.830 33351 Z= 0.264 Chirality : 0.051 0.572 3990 Planarity : 0.003 0.049 4221 Dihedral : 7.543 93.865 4473 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.51 % Allowed : 15.37 % Favored : 83.12 % 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: 0.10 (0.15), residues: 2901 helix: 1.81 (0.20), residues: 708 sheet: -0.23 (0.19), residues: 660 loop : -0.60 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.001 0.000 HIS C1064 PHE 0.021 0.001 PHE A 201 TYR 0.021 0.001 TYR B 904 ARG 0.003 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 2.962 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: symmetry clash REVERT: A 33 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8704 (p) REVERT: A 104 TRP cc_start: 0.8507 (m-90) cc_final: 0.8114 (m-90) REVERT: A 354 ASN cc_start: 0.9240 (t0) cc_final: 0.8927 (t0) REVERT: A 369 TYR cc_start: 0.8190 (t80) cc_final: 0.7909 (t80) REVERT: A 759 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8289 (t80) REVERT: A 960 ASN cc_start: 0.8268 (m-40) cc_final: 0.8037 (t0) REVERT: B 52 GLN cc_start: 0.8906 (tt0) cc_final: 0.8388 (tm-30) REVERT: B 269 TYR cc_start: 0.8462 (m-80) cc_final: 0.8065 (m-10) REVERT: B 354 ASN cc_start: 0.9150 (t0) cc_final: 0.8129 (p0) REVERT: B 508 TYR cc_start: 0.8693 (m-80) cc_final: 0.8254 (m-80) REVERT: B 740 MET cc_start: 0.8900 (tpp) cc_final: 0.8635 (tpp) REVERT: B 759 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8352 (t80) REVERT: C 33 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8790 (p) REVERT: C 52 GLN cc_start: 0.8885 (tt0) cc_final: 0.8497 (tm-30) REVERT: C 87 ASN cc_start: 0.8548 (m-40) cc_final: 0.7784 (p0) REVERT: C 104 TRP cc_start: 0.8742 (m-90) cc_final: 0.8357 (m-90) REVERT: C 354 ASN cc_start: 0.9211 (t0) cc_final: 0.8880 (t0) outliers start: 39 outliers final: 33 residues processed: 166 average time/residue: 0.2834 time to fit residues: 83.1282 Evaluate side-chains 166 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 269 optimal weight: 0.8980 chunk 233 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 180 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A 856 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 856 ASN C 501 ASN C 856 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24528 Z= 0.262 Angle : 0.582 11.747 33351 Z= 0.282 Chirality : 0.051 0.576 3990 Planarity : 0.003 0.049 4221 Dihedral : 7.455 95.571 4473 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.47 % Allowed : 15.49 % Favored : 83.04 % 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: 0.06 (0.15), residues: 2901 helix: 1.74 (0.20), residues: 699 sheet: -0.21 (0.18), residues: 690 loop : -0.62 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.003 0.001 HIS B1064 PHE 0.021 0.001 PHE A 201 TYR 0.023 0.001 TYR B 904 ARG 0.004 0.000 ARG B 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 2.539 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: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8799 (p) REVERT: A 369 TYR cc_start: 0.8295 (t80) cc_final: 0.8020 (t80) REVERT: A 759 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8114 (t80) REVERT: A 960 ASN cc_start: 0.8323 (m-40) cc_final: 0.7938 (t0) REVERT: B 52 GLN cc_start: 0.8942 (tt0) cc_final: 0.8393 (tm-30) REVERT: B 269 TYR cc_start: 0.8554 (m-80) cc_final: 0.8109 (m-10) REVERT: B 354 ASN cc_start: 0.9155 (t0) cc_final: 0.8148 (p0) REVERT: B 508 TYR cc_start: 0.8751 (m-80) cc_final: 0.8279 (m-80) REVERT: B 740 MET cc_start: 0.8923 (tpp) cc_final: 0.8667 (tpp) REVERT: B 759 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8361 (t80) REVERT: C 33 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8830 (p) REVERT: C 52 GLN cc_start: 0.8936 (tt0) cc_final: 0.8510 (tm-30) REVERT: C 87 ASN cc_start: 0.8564 (m-40) cc_final: 0.7774 (p0) REVERT: C 104 TRP cc_start: 0.8819 (m-90) cc_final: 0.8410 (m-90) REVERT: C 354 ASN cc_start: 0.9242 (t0) cc_final: 0.8962 (t0) REVERT: C 389 ASP cc_start: 0.8956 (m-30) cc_final: 0.8658 (m-30) REVERT: C 420 ASP cc_start: 0.8841 (p0) cc_final: 0.8536 (p0) outliers start: 38 outliers final: 31 residues processed: 162 average time/residue: 0.2866 time to fit residues: 81.4777 Evaluate side-chains 158 residues out of total 2589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 856 ASN B 926 GLN C 196 ASN C 856 ASN C 895 GLN C1106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.096594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.058534 restraints weight = 64270.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.061172 restraints weight = 28454.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.062854 restraints weight = 17713.409| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24528 Z= 0.334 Angle : 0.616 10.934 33351 Z= 0.301 Chirality : 0.052 0.584 3990 Planarity : 0.004 0.050 4221 Dihedral : 7.545 98.171 4473 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.51 % Allowed : 15.49 % Favored : 83.01 % 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 (0.15), residues: 2901 helix: 1.52 (0.20), residues: 699 sheet: -0.23 (0.18), residues: 675 loop : -0.56 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.004 0.001 HIS A1058 PHE 0.025 0.001 PHE A 855 TYR 0.023 0.001 TYR B 904 ARG 0.004 0.000 ARG B 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3504.70 seconds wall clock time: 66 minutes 20.36 seconds (3980.36 seconds total)