Starting phenix.real_space_refine on Wed Feb 21 07:54:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm9_27531/02_2024/8dm9_27531.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm9_27531/02_2024/8dm9_27531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm9_27531/02_2024/8dm9_27531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm9_27531/02_2024/8dm9_27531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm9_27531/02_2024/8dm9_27531.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm9_27531/02_2024/8dm9_27531.pdb" } resolution = 2.56 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= -0.001 sd= 0.024 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 140 5.16 5 C 19142 2.51 5 N 4922 2.21 5 O 5800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30004 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "B" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "C" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "D" Number of atoms: 4833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4833 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 15.10, per 1000 atoms: 0.50 Number of scatterers: 30004 At special positions: 0 Unit cell: (135, 157, 237, 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 140 16.00 O 5800 8.00 N 4922 7.00 C 19142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.05 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 546 " " NAG E 1 " - " ASN A 17 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 17 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.25 Conformation dependent library (CDL) restraints added in 4.9 seconds 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6944 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 49 sheets defined 32.3% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 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 365 through 370 removed outlier: 3.645A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.612A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.503A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.093A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.590A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.940A 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 945 through 965 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 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.969A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.943A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.873A pdb=" N LEU B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.718A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.871A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.861A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.587A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.744A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.981A 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 945 through 965 removed outlier: 3.552A 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 984 removed outlier: 3.501A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.044A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.954A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.772A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.861A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.555A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.889A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.605A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.992A 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 945 through 965 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 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.099A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 21 through 52 removed outlier: 4.259A pdb=" N GLN D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.609A pdb=" N THR D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.837A pdb=" N GLU D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.769A pdb=" N SER D 106 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 144 through 155 removed outlier: 5.327A pdb=" N ASP D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 193 removed outlier: 5.354A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.693A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 231 removed outlier: 3.652A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.755A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.534A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.724A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 4.194A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.575A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.473A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.757A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.303A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.018A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.949A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.587A 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: 3.775A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.970A 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: 3.754A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.108A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.739A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.868A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 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 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.874A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.802A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.952A 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: 6.577A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.319A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.703A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.103A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.055A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.839A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 133 through 142 removed outlier: 6.495A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.562A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.979A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.178A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.995A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.971A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.589A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.888A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.464A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.487A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.487A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.388A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.235A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.030A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.823A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 133 through 142 removed outlier: 6.536A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.569A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.328A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.011A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.993A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.152A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.811A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.863A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.513A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.513A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.352A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'D' and resid 131 through 132 removed outlier: 4.100A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.906A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.289A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1327 hydrogen bonds defined for protein. 3735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.94 Time building geometry restraints manager: 12.16 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: 9473 1.35 - 1.48: 8077 1.48 - 1.60: 12973 1.60 - 1.73: 0 1.73 - 1.86: 188 Bond restraints: 30711 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.08e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.97e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.93e+00 ... (remaining 30706 not shown) Histogram of bond angle deviations from ideal: 96.83 - 104.28: 562 104.28 - 111.72: 13853 111.72 - 119.16: 10817 119.16 - 126.61: 16117 126.61 - 134.05: 415 Bond angle restraints: 41764 Sorted by residual: angle pdb=" N ALA C 372 " pdb=" CA ALA C 372 " pdb=" C ALA C 372 " ideal model delta sigma weight residual 109.81 124.34 -14.53 2.21e+00 2.05e-01 4.32e+01 angle pdb=" CB ARG A 995 " pdb=" CG ARG A 995 " pdb=" CD ARG A 995 " ideal model delta sigma weight residual 111.30 125.46 -14.16 2.30e+00 1.89e-01 3.79e+01 angle pdb=" N ALA B 372 " pdb=" CA ALA B 372 " pdb=" C ALA B 372 " ideal model delta sigma weight residual 109.81 121.45 -11.64 2.21e+00 2.05e-01 2.78e+01 angle pdb=" C LEU A 335 " pdb=" N CYS A 336 " pdb=" CA CYS A 336 " ideal model delta sigma weight residual 120.51 128.02 -7.51 1.45e+00 4.76e-01 2.69e+01 angle pdb=" CA PRO C 373 " pdb=" N PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 112.00 105.16 6.84 1.40e+00 5.10e-01 2.39e+01 ... (remaining 41759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 17548 17.82 - 35.63: 1239 35.63 - 53.45: 230 53.45 - 71.27: 77 71.27 - 89.08: 36 Dihedral angle restraints: 19130 sinusoidal: 8359 harmonic: 10771 Sorted by residual: dihedral pdb=" CA CYS D 133 " pdb=" C CYS D 133 " pdb=" N ASN D 134 " pdb=" CA ASN D 134 " ideal model delta harmonic sigma weight residual -180.00 -138.91 -41.09 0 5.00e+00 4.00e-02 6.75e+01 dihedral pdb=" CA CYS D 141 " pdb=" C CYS D 141 " pdb=" N LEU D 142 " pdb=" CA LEU D 142 " ideal model delta harmonic sigma weight residual -180.00 -147.94 -32.06 0 5.00e+00 4.00e-02 4.11e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual 180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 19127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4049 0.081 - 0.161: 732 0.161 - 0.242: 53 0.242 - 0.322: 6 0.322 - 0.403: 3 Chirality restraints: 4843 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 4840 not shown) Planarity restraints: 5361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.063 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO C 373 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 955 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C ASN B 955 " -0.064 2.00e-02 2.50e+03 pdb=" O ASN B 955 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA B 956 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 952 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" C VAL B 952 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL B 952 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN B 953 " -0.020 2.00e-02 2.50e+03 ... (remaining 5358 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6885 2.79 - 3.32: 25827 3.32 - 3.85: 51297 3.85 - 4.37: 59124 4.37 - 4.90: 102185 Nonbonded interactions: 245318 Sorted by model distance: nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR B 396 " pdb=" O PRO C 230 " model vdw 2.267 2.440 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.269 2.440 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.270 2.440 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.273 2.440 ... (remaining 245313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 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: 14.850 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 77.090 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.390 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:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 0.005 0.080 30711 Z= 0.332 Angle : 0.879 14.531 41764 Z= 0.485 Chirality : 0.059 0.403 4843 Planarity : 0.007 0.092 5317 Dihedral : 13.279 89.082 12054 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.04 % Favored : 97.91 % Rotamer: Outliers : 0.15 % Allowed : 3.46 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.12), residues: 3633 helix: 0.28 (0.14), residues: 1050 sheet: 0.95 (0.19), residues: 668 loop : -0.75 (0.13), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 886 HIS 0.033 0.002 HIS A 954 PHE 0.040 0.003 PHE B 981 TYR 0.036 0.003 TYR B1067 ARG 0.027 0.001 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 397 time to evaluate : 3.450 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 66 HIS cc_start: 0.5780 (m90) cc_final: 0.5005 (m90) REVERT: A 129 LYS cc_start: 0.6348 (mtmt) cc_final: 0.6089 (mmmt) REVERT: A 140 PHE cc_start: 0.6108 (p90) cc_final: 0.5813 (p90) REVERT: A 170 TYR cc_start: 0.7589 (t80) cc_final: 0.7367 (t80) REVERT: A 338 PHE cc_start: 0.6724 (m-10) cc_final: 0.6434 (m-80) REVERT: A 549 THR cc_start: 0.7004 (m) cc_final: 0.6584 (m) REVERT: A 981 PHE cc_start: 0.7072 (m-80) cc_final: 0.6820 (m-10) REVERT: A 988 GLU cc_start: 0.7629 (pm20) cc_final: 0.7230 (pm20) REVERT: B 387 LEU cc_start: 0.7684 (mt) cc_final: 0.7479 (mt) REVERT: B 856 LYS cc_start: 0.5451 (mttt) cc_final: 0.4914 (pmtt) REVERT: B 981 PHE cc_start: 0.7645 (m-80) cc_final: 0.7100 (m-80) REVERT: B 1029 MET cc_start: 0.9269 (tpp) cc_final: 0.8938 (tpp) REVERT: C 88 ASP cc_start: 0.8018 (m-30) cc_final: 0.7480 (p0) REVERT: C 242 LEU cc_start: 0.6889 (mt) cc_final: 0.6682 (tp) REVERT: C 271 GLN cc_start: 0.8414 (mp10) cc_final: 0.8030 (mp10) REVERT: C 913 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8356 (pt0) REVERT: C 988 GLU cc_start: 0.8566 (mp0) cc_final: 0.8145 (mp0) REVERT: D 35 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6581 (tp30) REVERT: D 45 LEU cc_start: 0.5304 (tp) cc_final: 0.5024 (pp) REVERT: D 312 GLU cc_start: 0.5692 (tt0) cc_final: 0.4717 (pp20) REVERT: D 455 MET cc_start: 0.4242 (ttt) cc_final: 0.3827 (tpt) REVERT: D 474 MET cc_start: -0.0192 (mmp) cc_final: -0.1167 (mmm) REVERT: D 508 ASN cc_start: 0.4732 (m-40) cc_final: 0.4348 (m-40) REVERT: D 555 LEU cc_start: 0.3308 (mt) cc_final: 0.3101 (tm) REVERT: D 578 ASN cc_start: 0.4926 (t0) cc_final: 0.4348 (t0) REVERT: D 579 MET cc_start: 0.2237 (mtm) cc_final: 0.2032 (mmt) outliers start: 5 outliers final: 3 residues processed: 402 average time/residue: 1.3209 time to fit residues: 630.0454 Evaluate side-chains 179 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 913 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 9.9990 chunk 278 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 288 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 334 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 954 HIS B 317 ASN B 580 GLN B 606 ASN B 824 ASN C 66 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 370 ASN C 394 ASN C 954 HIS D 24 ASN D 220 ASN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30711 Z= 0.259 Angle : 0.609 22.079 41764 Z= 0.306 Chirality : 0.046 0.376 4843 Planarity : 0.005 0.069 5317 Dihedral : 7.242 59.556 5274 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.35 % Allowed : 8.37 % Favored : 89.29 % 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: 0.38 (0.13), residues: 3633 helix: 1.30 (0.16), residues: 1048 sheet: 0.69 (0.20), residues: 660 loop : -0.46 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 886 HIS 0.012 0.001 HIS A 954 PHE 0.020 0.002 PHE C 565 TYR 0.025 0.002 TYR C 200 ARG 0.008 0.001 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 188 time to evaluate : 3.267 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 17 ASN cc_start: 0.4207 (OUTLIER) cc_final: 0.3835 (m110) REVERT: A 133 PHE cc_start: 0.5948 (m-80) cc_final: 0.5707 (m-80) REVERT: A 140 PHE cc_start: 0.6210 (p90) cc_final: 0.5994 (p90) REVERT: A 190 ARG cc_start: 0.7046 (mmt90) cc_final: 0.6709 (mmt90) REVERT: A 238 PHE cc_start: 0.7305 (p90) cc_final: 0.6631 (p90) REVERT: A 339 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.6214 (t0) REVERT: A 342 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.7045 (t80) REVERT: A 985 ASP cc_start: 0.8185 (m-30) cc_final: 0.7304 (m-30) REVERT: A 988 GLU cc_start: 0.7768 (pm20) cc_final: 0.7379 (pm20) REVERT: A 1010 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7857 (mp10) REVERT: A 1145 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7673 (mm) REVERT: B 66 HIS cc_start: 0.7090 (t-90) cc_final: 0.6863 (t-90) REVERT: B 140 PHE cc_start: 0.7554 (p90) cc_final: 0.7270 (p90) REVERT: B 153 MET cc_start: 0.3369 (OUTLIER) cc_final: 0.2856 (pmm) REVERT: B 856 LYS cc_start: 0.5619 (mttt) cc_final: 0.5019 (pmtt) REVERT: B 969 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8887 (ttmm) REVERT: C 65 PHE cc_start: 0.7814 (m-80) cc_final: 0.7552 (m-10) REVERT: C 88 ASP cc_start: 0.8111 (m-30) cc_final: 0.7670 (p0) REVERT: C 334 ASN cc_start: 0.7140 (t0) cc_final: 0.6889 (p0) REVERT: C 362 VAL cc_start: 0.6806 (OUTLIER) cc_final: 0.6480 (m) REVERT: C 403 ARG cc_start: 0.7460 (mtp180) cc_final: 0.7020 (ttm-80) REVERT: C 985 ASP cc_start: 0.7777 (p0) cc_final: 0.7542 (m-30) REVERT: D 35 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6497 (tp30) REVERT: D 78 LYS cc_start: 0.6508 (mmtp) cc_final: 0.6038 (mtpm) REVERT: D 298 MET cc_start: 0.2844 (OUTLIER) cc_final: 0.2593 (mpt) REVERT: D 376 MET cc_start: 0.3922 (tpp) cc_final: 0.3556 (tpp) REVERT: D 455 MET cc_start: 0.4180 (ttt) cc_final: 0.2751 (tpt) REVERT: D 555 LEU cc_start: 0.3522 (mt) cc_final: 0.3085 (tm) REVERT: D 578 ASN cc_start: 0.5189 (t0) cc_final: 0.4860 (m-40) outliers start: 76 outliers final: 25 residues processed: 247 average time/residue: 1.1542 time to fit residues: 347.9808 Evaluate side-chains 188 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 298 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 185 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 278 optimal weight: 0.0570 chunk 227 optimal weight: 4.9990 chunk 92 optimal weight: 0.2980 chunk 334 optimal weight: 0.5980 chunk 361 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 chunk 331 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 268 optimal weight: 1.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN D 239 HIS D 345 HIS D 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30711 Z= 0.167 Angle : 0.543 21.575 41764 Z= 0.272 Chirality : 0.043 0.262 4843 Planarity : 0.004 0.059 5317 Dihedral : 6.400 58.987 5263 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.88 % Allowed : 10.06 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.13), residues: 3633 helix: 1.72 (0.16), residues: 1058 sheet: 0.65 (0.20), residues: 613 loop : -0.37 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 353 HIS 0.006 0.001 HIS B 954 PHE 0.023 0.001 PHE A 338 TYR 0.030 0.001 TYR D 215 ARG 0.008 0.000 ARG D 577 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 174 time to evaluate : 3.374 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 17 ASN cc_start: 0.4139 (OUTLIER) cc_final: 0.3847 (m-40) REVERT: A 66 HIS cc_start: 0.6907 (m-70) cc_final: 0.6624 (m90) REVERT: A 133 PHE cc_start: 0.6197 (m-80) cc_final: 0.5920 (m-80) REVERT: A 153 MET cc_start: 0.4510 (pp-130) cc_final: 0.4255 (ppp) REVERT: A 190 ARG cc_start: 0.6952 (mmt90) cc_final: 0.6668 (mmt90) REVERT: A 238 PHE cc_start: 0.7241 (p90) cc_final: 0.6691 (p90) REVERT: A 342 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.6975 (t80) REVERT: A 985 ASP cc_start: 0.7927 (m-30) cc_final: 0.7491 (m-30) REVERT: A 988 GLU cc_start: 0.7758 (pm20) cc_final: 0.7368 (pm20) REVERT: A 1010 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: B 66 HIS cc_start: 0.7104 (t-90) cc_final: 0.6886 (t-90) REVERT: B 105 ILE cc_start: 0.7881 (mp) cc_final: 0.7452 (pt) REVERT: B 140 PHE cc_start: 0.7753 (p90) cc_final: 0.7454 (p90) REVERT: B 153 MET cc_start: 0.3400 (OUTLIER) cc_final: 0.2780 (pmm) REVERT: B 540 ASN cc_start: 0.6510 (OUTLIER) cc_final: 0.6145 (p0) REVERT: B 856 LYS cc_start: 0.5663 (mttt) cc_final: 0.5043 (pmtt) REVERT: B 981 PHE cc_start: 0.7373 (m-80) cc_final: 0.7158 (m-10) REVERT: B 990 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: B 1092 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: C 52 GLN cc_start: 0.8069 (tp40) cc_final: 0.7491 (tp40) REVERT: C 88 ASP cc_start: 0.8071 (m-30) cc_final: 0.7738 (p0) REVERT: C 153 MET cc_start: 0.3900 (pp-130) cc_final: 0.3632 (pp-130) REVERT: C 158 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6614 (ptp-110) REVERT: C 189 LEU cc_start: 0.8617 (tp) cc_final: 0.8402 (tm) REVERT: C 190 ARG cc_start: 0.7814 (mtt90) cc_final: 0.7226 (mtt180) REVERT: C 242 LEU cc_start: 0.5812 (tp) cc_final: 0.5430 (mt) REVERT: C 362 VAL cc_start: 0.6988 (p) cc_final: 0.6776 (m) REVERT: C 403 ARG cc_start: 0.7642 (mtp180) cc_final: 0.7330 (ttm170) REVERT: D 35 GLU cc_start: 0.6694 (mt-10) cc_final: 0.6486 (tp30) REVERT: D 78 LYS cc_start: 0.6267 (mmtp) cc_final: 0.6024 (mtpm) REVERT: D 249 MET cc_start: 0.2867 (OUTLIER) cc_final: 0.2572 (tpt) REVERT: D 455 MET cc_start: 0.4191 (ttt) cc_final: 0.2855 (tpt) REVERT: D 474 MET cc_start: -0.1559 (OUTLIER) cc_final: -0.1772 (mmm) REVERT: D 555 LEU cc_start: 0.3518 (mt) cc_final: 0.3114 (tm) REVERT: D 557 MET cc_start: 0.1063 (tmm) cc_final: -0.0657 (ttp) REVERT: D 578 ASN cc_start: 0.5589 (t0) cc_final: 0.5115 (t0) REVERT: D 579 MET cc_start: 0.1581 (mtp) cc_final: 0.1348 (mmt) outliers start: 61 outliers final: 23 residues processed: 217 average time/residue: 1.2318 time to fit residues: 325.1195 Evaluate side-chains 187 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 480 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 330 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 159 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 335 optimal weight: 0.6980 chunk 355 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 chunk 318 optimal weight: 30.0000 chunk 95 optimal weight: 3.9990 overall best weight: 1.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 188 ASN A 360 ASN A 824 ASN B 779 GLN C 505 HIS C 824 ASN C 926 GLN D 42 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30711 Z= 0.279 Angle : 0.581 20.659 41764 Z= 0.291 Chirality : 0.045 0.254 4843 Planarity : 0.004 0.059 5317 Dihedral : 6.060 58.324 5263 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.44 % Allowed : 10.40 % Favored : 87.16 % 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: 0.55 (0.13), residues: 3633 helix: 1.72 (0.16), residues: 1058 sheet: 0.29 (0.20), residues: 631 loop : -0.34 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.005 0.001 HIS B 954 PHE 0.019 0.002 PHE C 565 TYR 0.023 0.002 TYR A1067 ARG 0.005 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 169 time to evaluate : 3.247 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 133 PHE cc_start: 0.6314 (m-80) cc_final: 0.6048 (m-80) REVERT: A 170 TYR cc_start: 0.7838 (t80) cc_final: 0.7638 (t80) REVERT: A 339 ASP cc_start: 0.6850 (m-30) cc_final: 0.6431 (t0) REVERT: A 342 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7076 (t80) REVERT: A 985 ASP cc_start: 0.7902 (m-30) cc_final: 0.7450 (m-30) REVERT: A 988 GLU cc_start: 0.7761 (pm20) cc_final: 0.7404 (pm20) REVERT: A 1010 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: B 66 HIS cc_start: 0.6963 (t-90) cc_final: 0.6754 (t-90) REVERT: B 140 PHE cc_start: 0.7904 (p90) cc_final: 0.7582 (p90) REVERT: B 357 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6095 (pmm-80) REVERT: B 540 ASN cc_start: 0.6633 (OUTLIER) cc_final: 0.6235 (p0) REVERT: B 740 MET cc_start: 0.7524 (ttm) cc_final: 0.7202 (mtp) REVERT: B 856 LYS cc_start: 0.5806 (mttt) cc_final: 0.5011 (pmtt) REVERT: B 1092 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: C 88 ASP cc_start: 0.8153 (m-30) cc_final: 0.7797 (OUTLIER) REVERT: C 158 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6701 (ptp-110) REVERT: C 168 PHE cc_start: 0.6600 (t80) cc_final: 0.6252 (t80) REVERT: C 242 LEU cc_start: 0.5921 (tp) cc_final: 0.5485 (mt) REVERT: C 403 ARG cc_start: 0.7599 (mtp180) cc_final: 0.7379 (ttm170) REVERT: D 35 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6469 (tp30) REVERT: D 78 LYS cc_start: 0.6271 (mmtp) cc_final: 0.6048 (mtpm) REVERT: D 171 GLU cc_start: 0.2957 (OUTLIER) cc_final: 0.2711 (tm-30) REVERT: D 323 MET cc_start: -0.1163 (mmt) cc_final: -0.1628 (mpp) REVERT: D 387 ARG cc_start: 0.5172 (ptt90) cc_final: 0.4385 (mmm160) REVERT: D 455 MET cc_start: 0.4164 (ttt) cc_final: 0.2770 (tpt) REVERT: D 474 MET cc_start: -0.1213 (OUTLIER) cc_final: -0.1745 (mmm) REVERT: D 555 LEU cc_start: 0.3752 (mt) cc_final: 0.3334 (tm) REVERT: D 557 MET cc_start: 0.1026 (tmm) cc_final: -0.0451 (ttp) REVERT: D 578 ASN cc_start: 0.5302 (t0) cc_final: 0.4879 (t0) REVERT: D 579 MET cc_start: 0.1876 (mtp) cc_final: 0.1496 (mmt) outliers start: 79 outliers final: 28 residues processed: 231 average time/residue: 1.1867 time to fit residues: 335.9777 Evaluate side-chains 179 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 480 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 296 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 264 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 303 optimal weight: 1.9990 chunk 245 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 181 optimal weight: 0.6980 chunk 319 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 188 ASN A 409 GLN A 907 ASN C 505 HIS C 926 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 30711 Z= 0.198 Angle : 0.534 16.629 41764 Z= 0.268 Chirality : 0.044 0.262 4843 Planarity : 0.004 0.059 5317 Dihedral : 5.730 58.457 5263 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.13 % Allowed : 11.70 % Favored : 86.17 % 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: 0.64 (0.14), residues: 3633 helix: 1.91 (0.16), residues: 1052 sheet: 0.28 (0.20), residues: 618 loop : -0.32 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 163 HIS 0.004 0.001 HIS B 954 PHE 0.020 0.001 PHE B 981 TYR 0.021 0.001 TYR A1067 ARG 0.004 0.000 ARG D 518 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 163 time to evaluate : 3.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6253 (m-80) cc_final: 0.6014 (m-80) REVERT: A 170 TYR cc_start: 0.7765 (t80) cc_final: 0.7495 (t80) REVERT: A 190 ARG cc_start: 0.7097 (mmt90) cc_final: 0.6695 (mmt90) REVERT: A 197 ILE cc_start: 0.3742 (OUTLIER) cc_final: 0.3521 (mm) REVERT: A 339 ASP cc_start: 0.6821 (m-30) cc_final: 0.6317 (t0) REVERT: A 342 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7036 (t80) REVERT: A 985 ASP cc_start: 0.7878 (m-30) cc_final: 0.7428 (m-30) REVERT: A 988 GLU cc_start: 0.7796 (pm20) cc_final: 0.7421 (pm20) REVERT: B 105 ILE cc_start: 0.7814 (mp) cc_final: 0.7522 (pt) REVERT: B 140 PHE cc_start: 0.7898 (p90) cc_final: 0.7668 (p90) REVERT: B 357 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6235 (pmm150) REVERT: B 540 ASN cc_start: 0.6620 (OUTLIER) cc_final: 0.6225 (p0) REVERT: B 759 PHE cc_start: 0.7869 (t80) cc_final: 0.7592 (t80) REVERT: B 856 LYS cc_start: 0.5709 (mttt) cc_final: 0.4991 (pmtt) REVERT: B 1092 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: C 88 ASP cc_start: 0.8157 (m-30) cc_final: 0.7806 (OUTLIER) REVERT: C 158 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6641 (ptp-110) REVERT: C 168 PHE cc_start: 0.6577 (t80) cc_final: 0.6286 (t80) REVERT: C 190 ARG cc_start: 0.7861 (mtt90) cc_final: 0.7035 (mtt-85) REVERT: C 242 LEU cc_start: 0.5999 (tp) cc_final: 0.5718 (mt) REVERT: C 964 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8449 (mmmt) REVERT: D 35 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6460 (tp30) REVERT: D 78 LYS cc_start: 0.6282 (mmtp) cc_final: 0.6054 (mtpm) REVERT: D 141 CYS cc_start: -0.2587 (OUTLIER) cc_final: -0.3236 (m) REVERT: D 171 GLU cc_start: 0.2986 (OUTLIER) cc_final: 0.2777 (tm-30) REVERT: D 387 ARG cc_start: 0.5188 (ptt90) cc_final: 0.4391 (mmm160) REVERT: D 455 MET cc_start: 0.4205 (ttt) cc_final: 0.2768 (tpt) REVERT: D 474 MET cc_start: -0.1175 (OUTLIER) cc_final: -0.1636 (mmm) REVERT: D 483 GLU cc_start: 0.3857 (OUTLIER) cc_final: 0.3150 (pt0) REVERT: D 497 TYR cc_start: 0.0426 (m-80) cc_final: 0.0060 (m-10) REVERT: D 555 LEU cc_start: 0.3786 (mt) cc_final: 0.3314 (tm) REVERT: D 557 MET cc_start: 0.0878 (tmm) cc_final: -0.0456 (ttp) REVERT: D 578 ASN cc_start: 0.5301 (t0) cc_final: 0.4840 (t0) REVERT: D 579 MET cc_start: 0.1864 (mtp) cc_final: 0.1492 (mmt) outliers start: 69 outliers final: 31 residues processed: 220 average time/residue: 1.1992 time to fit residues: 325.1281 Evaluate side-chains 188 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 147 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 483 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 119 optimal weight: 5.9990 chunk 320 optimal weight: 40.0000 chunk 70 optimal weight: 0.4980 chunk 208 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 356 optimal weight: 8.9990 chunk 295 optimal weight: 0.5980 chunk 164 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 30711 Z= 0.318 Angle : 0.575 9.265 41764 Z= 0.293 Chirality : 0.046 0.256 4843 Planarity : 0.004 0.058 5317 Dihedral : 5.713 59.023 5263 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.44 % Allowed : 11.92 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3633 helix: 1.86 (0.16), residues: 1048 sheet: 0.27 (0.19), residues: 625 loop : -0.42 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 163 HIS 0.004 0.001 HIS A1088 PHE 0.018 0.002 PHE C 565 TYR 0.022 0.002 TYR A1067 ARG 0.009 0.001 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 162 time to evaluate : 3.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6335 (m-80) cc_final: 0.6097 (m-80) REVERT: A 190 ARG cc_start: 0.7247 (mmt90) cc_final: 0.6757 (mmt90) REVERT: A 342 PHE cc_start: 0.7497 (t80) cc_final: 0.7042 (t80) REVERT: A 592 PHE cc_start: 0.3945 (p90) cc_final: 0.3737 (p90) REVERT: A 985 ASP cc_start: 0.7907 (m-30) cc_final: 0.7425 (m-30) REVERT: A 988 GLU cc_start: 0.7834 (pm20) cc_final: 0.7486 (pm20) REVERT: B 105 ILE cc_start: 0.8148 (mp) cc_final: 0.7909 (pt) REVERT: B 226 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8399 (tp) REVERT: B 357 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6319 (pmm150) REVERT: B 540 ASN cc_start: 0.6623 (OUTLIER) cc_final: 0.6208 (p0) REVERT: B 759 PHE cc_start: 0.7915 (t80) cc_final: 0.7631 (t80) REVERT: B 1092 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: C 88 ASP cc_start: 0.8069 (m-30) cc_final: 0.7751 (OUTLIER) REVERT: C 158 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6667 (ptp-110) REVERT: C 168 PHE cc_start: 0.6625 (t80) cc_final: 0.6268 (t80) REVERT: C 190 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7154 (mtt-85) REVERT: C 242 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5816 (mt) REVERT: C 347 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.5484 (m-10) REVERT: C 964 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8488 (mmmt) REVERT: D 35 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6397 (tp30) REVERT: D 78 LYS cc_start: 0.6241 (mmtp) cc_final: 0.6015 (mtpm) REVERT: D 171 GLU cc_start: 0.2993 (OUTLIER) cc_final: 0.2769 (tm-30) REVERT: D 455 MET cc_start: 0.4330 (ttt) cc_final: 0.2935 (tpt) REVERT: D 473 TRP cc_start: 0.0718 (OUTLIER) cc_final: 0.0334 (m-10) REVERT: D 474 MET cc_start: -0.1180 (OUTLIER) cc_final: -0.1530 (mmm) REVERT: D 483 GLU cc_start: 0.3551 (OUTLIER) cc_final: 0.2886 (pt0) REVERT: D 555 LEU cc_start: 0.3800 (mt) cc_final: 0.3341 (tm) REVERT: D 578 ASN cc_start: 0.5264 (t0) cc_final: 0.4839 (t0) REVERT: D 579 MET cc_start: 0.1925 (mtp) cc_final: 0.1511 (mmt) outliers start: 79 outliers final: 35 residues processed: 226 average time/residue: 1.1595 time to fit residues: 321.1224 Evaluate side-chains 188 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 142 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 473 TRP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 483 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 343 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 202 optimal weight: 0.7980 chunk 260 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 299 optimal weight: 0.6980 chunk 198 optimal weight: 0.5980 chunk 354 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 216 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30711 Z= 0.171 Angle : 0.536 17.300 41764 Z= 0.268 Chirality : 0.043 0.269 4843 Planarity : 0.004 0.056 5317 Dihedral : 5.410 59.079 5263 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.67 % Allowed : 13.12 % Favored : 85.21 % 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: 0.65 (0.14), residues: 3633 helix: 1.98 (0.16), residues: 1052 sheet: 0.27 (0.19), residues: 655 loop : -0.35 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 104 HIS 0.003 0.000 HIS B 954 PHE 0.039 0.001 PHE C 186 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG D 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 158 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6287 (m-80) cc_final: 0.6051 (m-80) REVERT: A 170 TYR cc_start: 0.7649 (t80) cc_final: 0.7302 (t80) REVERT: A 190 ARG cc_start: 0.7181 (mmt90) cc_final: 0.6699 (mmt90) REVERT: A 339 ASP cc_start: 0.6939 (m-30) cc_final: 0.6419 (t0) REVERT: A 342 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.7082 (t80) REVERT: A 985 ASP cc_start: 0.7884 (m-30) cc_final: 0.7403 (m-30) REVERT: A 988 GLU cc_start: 0.7831 (pm20) cc_final: 0.7485 (pm20) REVERT: B 540 ASN cc_start: 0.6637 (OUTLIER) cc_final: 0.6243 (p0) REVERT: B 856 LYS cc_start: 0.5355 (OUTLIER) cc_final: 0.4783 (pmtt) REVERT: C 88 ASP cc_start: 0.8049 (m-30) cc_final: 0.7730 (OUTLIER) REVERT: C 129 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.6314 (mmtm) REVERT: C 158 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6680 (ptp-110) REVERT: C 190 ARG cc_start: 0.7949 (mtt90) cc_final: 0.7160 (mtt-85) REVERT: C 347 PHE cc_start: 0.6325 (OUTLIER) cc_final: 0.5452 (m-10) REVERT: D 35 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6396 (tp30) REVERT: D 78 LYS cc_start: 0.6262 (mmtp) cc_final: 0.6004 (mtpm) REVERT: D 142 LEU cc_start: 0.1280 (OUTLIER) cc_final: 0.0309 (mp) REVERT: D 171 GLU cc_start: 0.2999 (OUTLIER) cc_final: 0.2785 (tm-30) REVERT: D 455 MET cc_start: 0.4308 (ttt) cc_final: 0.2886 (tpt) REVERT: D 474 MET cc_start: -0.1148 (mmm) cc_final: -0.1423 (mmm) REVERT: D 483 GLU cc_start: 0.3509 (OUTLIER) cc_final: 0.2808 (pt0) REVERT: D 497 TYR cc_start: 0.0165 (m-80) cc_final: -0.0059 (m-10) REVERT: D 555 LEU cc_start: 0.3801 (mt) cc_final: 0.3319 (tm) REVERT: D 557 MET cc_start: 0.1034 (tmm) cc_final: -0.0606 (ttp) REVERT: D 578 ASN cc_start: 0.5314 (t0) cc_final: 0.4833 (t0) REVERT: D 579 MET cc_start: 0.1829 (mtp) cc_final: 0.1398 (mmt) outliers start: 54 outliers final: 28 residues processed: 200 average time/residue: 1.2126 time to fit residues: 299.6124 Evaluate side-chains 179 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 143 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 483 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 219 optimal weight: 4.9990 chunk 141 optimal weight: 30.0000 chunk 211 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 225 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 278 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 907 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30711 Z= 0.318 Angle : 0.594 14.553 41764 Z= 0.299 Chirality : 0.046 0.257 4843 Planarity : 0.004 0.056 5317 Dihedral : 5.619 59.897 5263 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.76 % Allowed : 13.62 % Favored : 84.62 % 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: 0.52 (0.14), residues: 3633 helix: 1.92 (0.16), residues: 1052 sheet: 0.07 (0.20), residues: 605 loop : -0.41 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 104 HIS 0.004 0.001 HIS A1048 PHE 0.026 0.002 PHE C 186 TYR 0.022 0.001 TYR C1067 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 149 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.5724 (m-80) cc_final: 0.5388 (m-80) REVERT: A 170 TYR cc_start: 0.7612 (t80) cc_final: 0.7224 (t80) REVERT: A 190 ARG cc_start: 0.7330 (mmt90) cc_final: 0.7090 (mmt90) REVERT: A 342 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.7094 (t80) REVERT: A 592 PHE cc_start: 0.4704 (p90) cc_final: 0.4439 (p90) REVERT: A 985 ASP cc_start: 0.7912 (m-30) cc_final: 0.7436 (m-30) REVERT: A 988 GLU cc_start: 0.7866 (pm20) cc_final: 0.7507 (pm20) REVERT: B 540 ASN cc_start: 0.6627 (OUTLIER) cc_final: 0.6215 (p0) REVERT: C 88 ASP cc_start: 0.8112 (m-30) cc_final: 0.7793 (OUTLIER) REVERT: C 153 MET cc_start: 0.3422 (pmm) cc_final: 0.3182 (pmm) REVERT: C 158 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6533 (ptp-110) REVERT: C 190 ARG cc_start: 0.8076 (mtt90) cc_final: 0.7484 (mtt-85) REVERT: C 347 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.5525 (m-10) REVERT: C 492 LEU cc_start: 0.7963 (mt) cc_final: 0.7423 (mp) REVERT: C 964 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8528 (mmmt) REVERT: D 35 GLU cc_start: 0.6613 (mt-10) cc_final: 0.6354 (tp30) REVERT: D 78 LYS cc_start: 0.6263 (mmtp) cc_final: 0.6008 (mtpm) REVERT: D 142 LEU cc_start: 0.1329 (OUTLIER) cc_final: 0.0290 (mp) REVERT: D 455 MET cc_start: 0.4361 (ttt) cc_final: 0.2966 (tpt) REVERT: D 474 MET cc_start: -0.1293 (OUTLIER) cc_final: -0.1562 (mmm) REVERT: D 483 GLU cc_start: 0.3887 (OUTLIER) cc_final: 0.3188 (pt0) REVERT: D 557 MET cc_start: 0.1229 (tmm) cc_final: -0.0425 (ttp) REVERT: D 578 ASN cc_start: 0.5264 (t0) cc_final: 0.4787 (t0) REVERT: D 579 MET cc_start: 0.1712 (mtp) cc_final: 0.1278 (mmt) outliers start: 57 outliers final: 27 residues processed: 195 average time/residue: 1.2987 time to fit residues: 315.9152 Evaluate side-chains 174 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 483 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 322 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 310 optimal weight: 20.0000 chunk 330 optimal weight: 7.9990 chunk 198 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 259 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 312 optimal weight: 20.0000 chunk 329 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30711 Z= 0.268 Angle : 0.580 14.872 41764 Z= 0.290 Chirality : 0.045 0.262 4843 Planarity : 0.004 0.054 5317 Dihedral : 5.614 59.788 5263 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.67 % Allowed : 14.14 % Favored : 84.19 % 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: 0.50 (0.14), residues: 3633 helix: 1.96 (0.16), residues: 1049 sheet: 0.05 (0.19), residues: 604 loop : -0.44 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 104 HIS 0.004 0.001 HIS B 954 PHE 0.027 0.001 PHE C 186 TYR 0.021 0.001 TYR A1067 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 142 time to evaluate : 3.513 Fit side-chains revert: symmetry clash REVERT: A 106 PHE cc_start: 0.5759 (m-80) cc_final: 0.5379 (m-80) REVERT: A 170 TYR cc_start: 0.7652 (t80) cc_final: 0.7389 (t80) REVERT: A 190 ARG cc_start: 0.7306 (mmt90) cc_final: 0.7061 (mmt90) REVERT: A 342 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.7146 (t80) REVERT: A 592 PHE cc_start: 0.4970 (p90) cc_final: 0.4647 (p90) REVERT: A 985 ASP cc_start: 0.7826 (m-30) cc_final: 0.7370 (m-30) REVERT: A 988 GLU cc_start: 0.7880 (pm20) cc_final: 0.7511 (pm20) REVERT: B 105 ILE cc_start: 0.7834 (mp) cc_final: 0.7546 (pt) REVERT: B 540 ASN cc_start: 0.6579 (OUTLIER) cc_final: 0.6195 (p0) REVERT: B 856 LYS cc_start: 0.5506 (mtmm) cc_final: 0.5268 (mtmm) REVERT: C 88 ASP cc_start: 0.8140 (m-30) cc_final: 0.7817 (OUTLIER) REVERT: C 153 MET cc_start: 0.3145 (pmm) cc_final: 0.2898 (pmm) REVERT: C 158 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6555 (ptp-110) REVERT: C 190 ARG cc_start: 0.7972 (mtt90) cc_final: 0.7540 (mtt-85) REVERT: C 347 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.5556 (m-10) REVERT: C 498 ARG cc_start: 0.7159 (mpp80) cc_final: 0.6674 (mpt90) REVERT: C 964 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8459 (mmmt) REVERT: D 35 GLU cc_start: 0.6597 (mt-10) cc_final: 0.6344 (tp30) REVERT: D 78 LYS cc_start: 0.6311 (mmtp) cc_final: 0.6016 (mtpm) REVERT: D 142 LEU cc_start: 0.1398 (OUTLIER) cc_final: 0.0478 (mp) REVERT: D 455 MET cc_start: 0.4316 (ttt) cc_final: 0.2921 (tpt) REVERT: D 474 MET cc_start: -0.1218 (OUTLIER) cc_final: -0.1502 (mmm) REVERT: D 480 MET cc_start: 0.2948 (mpt) cc_final: 0.2493 (mpt) REVERT: D 483 GLU cc_start: 0.3872 (OUTLIER) cc_final: 0.3173 (pt0) REVERT: D 557 MET cc_start: 0.1666 (tmm) cc_final: 0.0033 (ttp) REVERT: D 578 ASN cc_start: 0.5203 (t0) cc_final: 0.4751 (t0) REVERT: D 579 MET cc_start: 0.1836 (mtp) cc_final: 0.1295 (mmt) outliers start: 54 outliers final: 30 residues processed: 187 average time/residue: 1.0925 time to fit residues: 255.8823 Evaluate side-chains 176 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 483 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 217 optimal weight: 4.9990 chunk 349 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 chunk 165 optimal weight: 0.4980 chunk 242 optimal weight: 10.0000 chunk 366 optimal weight: 7.9990 chunk 337 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 179 optimal weight: 0.5980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN D 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 30711 Z= 0.340 Angle : 0.615 14.594 41764 Z= 0.308 Chirality : 0.046 0.249 4843 Planarity : 0.004 0.055 5317 Dihedral : 5.814 59.942 5263 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.30 % Allowed : 14.63 % Favored : 84.07 % 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: 0.41 (0.14), residues: 3633 helix: 1.88 (0.16), residues: 1054 sheet: -0.07 (0.19), residues: 605 loop : -0.48 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 104 HIS 0.004 0.001 HIS B 954 PHE 0.030 0.002 PHE A 133 TYR 0.022 0.002 TYR A1067 ARG 0.004 0.001 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 145 time to evaluate : 3.261 Fit side-chains revert: symmetry clash REVERT: A 106 PHE cc_start: 0.5741 (m-80) cc_final: 0.5431 (m-80) REVERT: A 170 TYR cc_start: 0.7712 (t80) cc_final: 0.7436 (t80) REVERT: A 190 ARG cc_start: 0.7297 (mmt90) cc_final: 0.7005 (mmt90) REVERT: A 342 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7103 (t80) REVERT: A 985 ASP cc_start: 0.7964 (m-30) cc_final: 0.7388 (m-30) REVERT: A 988 GLU cc_start: 0.7901 (pm20) cc_final: 0.7520 (pm20) REVERT: B 105 ILE cc_start: 0.7854 (mp) cc_final: 0.7522 (pt) REVERT: B 540 ASN cc_start: 0.6568 (OUTLIER) cc_final: 0.6162 (p0) REVERT: B 856 LYS cc_start: 0.5487 (mtmm) cc_final: 0.5272 (mtmm) REVERT: C 88 ASP cc_start: 0.8182 (m-30) cc_final: 0.7838 (OUTLIER) REVERT: C 153 MET cc_start: 0.3649 (pmm) cc_final: 0.3412 (pmm) REVERT: C 158 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.6376 (ptp-110) REVERT: C 190 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7529 (mtt-85) REVERT: C 347 PHE cc_start: 0.6701 (OUTLIER) cc_final: 0.5630 (m-10) REVERT: C 498 ARG cc_start: 0.7124 (mpp80) cc_final: 0.6835 (tpp-160) REVERT: C 964 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8509 (mmmt) REVERT: D 35 GLU cc_start: 0.6628 (mt-10) cc_final: 0.6323 (tp30) REVERT: D 78 LYS cc_start: 0.6211 (mmtp) cc_final: 0.5969 (mtpm) REVERT: D 142 LEU cc_start: 0.1353 (OUTLIER) cc_final: 0.0337 (mp) REVERT: D 249 MET cc_start: 0.2818 (tpt) cc_final: 0.2536 (tpt) REVERT: D 455 MET cc_start: 0.4352 (ttt) cc_final: 0.2876 (tpt) REVERT: D 480 MET cc_start: 0.2862 (mpt) cc_final: 0.2329 (mpt) REVERT: D 483 GLU cc_start: 0.3870 (OUTLIER) cc_final: 0.3168 (pt0) REVERT: D 557 MET cc_start: 0.1706 (tmm) cc_final: 0.0042 (ttp) REVERT: D 578 ASN cc_start: 0.5267 (t0) cc_final: 0.4861 (t0) REVERT: D 579 MET cc_start: 0.2076 (mtp) cc_final: 0.1460 (mmt) outliers start: 42 outliers final: 30 residues processed: 176 average time/residue: 1.1144 time to fit residues: 245.3788 Evaluate side-chains 180 residues out of total 3239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 483 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 231 optimal weight: 5.9990 chunk 310 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 chunk 269 optimal weight: 0.0980 chunk 43 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 300 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.157393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.094242 restraints weight = 60147.935| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.18 r_work: 0.3129 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30711 Z= 0.197 Angle : 0.556 12.930 41764 Z= 0.278 Chirality : 0.044 0.260 4843 Planarity : 0.004 0.082 5317 Dihedral : 5.549 59.833 5263 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.23 % Allowed : 14.85 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3633 helix: 2.03 (0.16), residues: 1048 sheet: -0.05 (0.19), residues: 605 loop : -0.40 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 104 HIS 0.003 0.001 HIS B 954 PHE 0.030 0.001 PHE B 140 TYR 0.023 0.001 TYR C 170 ARG 0.004 0.000 ARG B 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10038.49 seconds wall clock time: 180 minutes 34.60 seconds (10834.60 seconds total)