Starting phenix.real_space_refine on Tue Feb 20 17:41:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxz_25511/02_2024/7sxz_25511.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxz_25511/02_2024/7sxz_25511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxz_25511/02_2024/7sxz_25511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxz_25511/02_2024/7sxz_25511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxz_25511/02_2024/7sxz_25511.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxz_25511/02_2024/7sxz_25511.pdb" } resolution = 2.61 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= 0.039 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 132 5.16 5 C 18191 2.51 5 N 4679 2.21 5 O 5581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "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: 28583 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 6555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6555 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 45, 'TRANS': 795} Chain breaks: 8 Chain: "B" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 14.18, per 1000 atoms: 0.50 Number of scatterers: 28583 At special positions: 0 Unit cell: (141, 158, 236, 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 132 16.00 O 5581 8.00 N 4679 7.00 C 18191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, 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 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 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=2.03 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 E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 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 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 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " " 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 " Time building additional restraints: 11.01 Conformation dependent library (CDL) restraints added in 4.7 seconds 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6604 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 42 sheets defined 33.2% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.28 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.890A 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: 3.640A 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: 3.942A 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 removed outlier: 3.564A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.265A 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 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.697A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.084A 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: 3.609A 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 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.927A 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 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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.047A 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: 3.839A 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: 3.842A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.895A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.611A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.549A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' 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: 3.598A 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 removed outlier: 3.549A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.888A 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 removed outlier: 3.503A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.118A 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 'E' and resid 20 through 53 removed outlier: 4.153A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.823A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.084A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 155 removed outlier: 3.988A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.706A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.700A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.796A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.548A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.684A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.252A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.529A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.388A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.768A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.447A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.875A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 78 through 79 current: chain 'A' and resid 188 through 197 removed outlier: 6.306A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.108A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.178A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.932A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 163 removed outlier: 9.490A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.279A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.210A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.114A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.596A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1078 removed outlier: 3.848A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.312A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.911A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 78 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 6.342A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.008A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 11.407A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.004A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.295A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.515A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 154 through 172 current: chain 'B' and resid 259 through 260 Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.708A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.146A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.250A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.123A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.820A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.886A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.259A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'C' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 79 current: chain 'C' and resid 188 through 197 removed outlier: 5.938A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.124A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 85 current: chain 'C' and resid 116 through 121 removed outlier: 3.585A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 154 through 172 current: chain 'C' and resid 259 through 260 Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.695A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.841A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.863A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.535A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.030A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1078 removed outlier: 3.912A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.327A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.752A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.939A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.333A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1148 hydrogen bonds defined for protein. 3228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.62 Time building geometry restraints manager: 11.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9009 1.34 - 1.47: 7369 1.47 - 1.59: 12683 1.59 - 1.72: 0 1.72 - 1.84: 180 Bond restraints: 29241 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.93e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.47e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.38e+00 ... (remaining 29236 not shown) Histogram of bond angle deviations from ideal: 97.65 - 104.93: 615 104.93 - 112.22: 14397 112.22 - 119.50: 9781 119.50 - 126.78: 14621 126.78 - 134.06: 373 Bond angle restraints: 39787 Sorted by residual: angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.82 129.36 -6.54 1.42e+00 4.96e-01 2.12e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.27 -5.57 1.22e+00 6.72e-01 2.08e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.23 -5.53 1.22e+00 6.72e-01 2.05e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 115.88 -5.18 1.22e+00 6.72e-01 1.81e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 122.06 -7.96 2.00e+00 2.50e-01 1.58e+01 ... (remaining 39782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16803 17.92 - 35.85: 1178 35.85 - 53.77: 177 53.77 - 71.70: 58 71.70 - 89.62: 36 Dihedral angle restraints: 18252 sinusoidal: 8006 harmonic: 10246 Sorted by residual: dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 154.55 25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -46.34 -39.66 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CA PHE C 515 " pdb=" C PHE C 515 " pdb=" N GLU C 516 " pdb=" CA GLU C 516 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 18249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3762 0.071 - 0.143: 799 0.143 - 0.214: 85 0.214 - 0.286: 6 0.286 - 0.357: 1 Chirality restraints: 4653 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 -2.04 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL B 576 " pdb=" CA VAL B 576 " pdb=" CG1 VAL B 576 " pdb=" CG2 VAL B 576 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 4650 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 394 " -0.035 2.00e-02 2.50e+03 7.13e-02 5.08e+01 pdb=" CG ASN C 394 " 0.123 2.00e-02 2.50e+03 pdb=" OD1 ASN C 394 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN C 394 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 36 " 0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C ALA E 36 " -0.072 2.00e-02 2.50e+03 pdb=" O ALA E 36 " 0.027 2.00e-02 2.50e+03 pdb=" N GLU E 37 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" C ARG E 169 " -0.053 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.020 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.018 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7451 2.80 - 3.33: 24622 3.33 - 3.85: 49344 3.85 - 4.38: 56706 4.38 - 4.90: 97196 Nonbonded interactions: 235319 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.280 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.291 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.292 2.440 nonbonded pdb=" OE1 GLN A 115 " pdb=" OG1 THR A 167 " model vdw 2.301 2.440 nonbonded pdb=" OD1 ASN A 540 " pdb=" OG1 THR A 549 " model vdw 2.305 2.440 ... (remaining 235314 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' 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: 4.730 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: 0.030 Extract box with map and model: 15.780 Check model and map are aligned: 0.380 Set scattering table: 0.250 Process input model: 72.360 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.330 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: 0.000 Load rotamer database and sin/cos tables:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 0.058 29241 Z= 0.319 Angle : 0.819 10.049 39787 Z= 0.446 Chirality : 0.057 0.357 4653 Planarity : 0.006 0.071 5070 Dihedral : 12.887 89.619 11528 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: -0.12 (0.13), residues: 3465 helix: 0.71 (0.14), residues: 1003 sheet: 0.55 (0.19), residues: 688 loop : -0.78 (0.13), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 886 HIS 0.007 0.001 HIS E 378 PHE 0.034 0.002 PHE A 238 TYR 0.033 0.002 TYR A 200 ARG 0.008 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 3.078 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 175 PHE cc_start: 0.5120 (m-10) cc_final: 0.4429 (m-10) REVERT: A 1029 MET cc_start: 0.9141 (tpp) cc_final: 0.8908 (tpp) REVERT: B 54 LEU cc_start: 0.9228 (mp) cc_final: 0.8804 (tp) REVERT: B 88 ASP cc_start: 0.8933 (m-30) cc_final: 0.8649 (p0) REVERT: B 153 MET cc_start: 0.5775 (ptt) cc_final: 0.4789 (pmt) REVERT: B 369 TYR cc_start: 0.8443 (t80) cc_final: 0.8080 (t80) REVERT: B 370 ASN cc_start: 0.8908 (m-40) cc_final: 0.7823 (p0) REVERT: C 565 PHE cc_start: 0.8149 (p90) cc_final: 0.7895 (p90) REVERT: E 341 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7729 (ptpp) REVERT: E 480 MET cc_start: 0.1418 (mtp) cc_final: 0.0923 (mpp) REVERT: E 559 ARG cc_start: 0.7420 (ptm-80) cc_final: 0.7186 (ttp80) outliers start: 0 outliers final: 2 residues processed: 290 average time/residue: 1.4259 time to fit residues: 482.0964 Evaluate side-chains 132 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain C residue 360 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 30.0000 chunk 266 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 275 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 318 optimal weight: 0.0870 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 926 GLN B 115 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 580 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 370 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN E 578 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29241 Z= 0.202 Angle : 0.539 9.015 39787 Z= 0.278 Chirality : 0.043 0.241 4653 Planarity : 0.004 0.054 5070 Dihedral : 5.349 59.275 5109 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.00 % Allowed : 7.94 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3465 helix: 1.73 (0.16), residues: 1029 sheet: 0.63 (0.20), residues: 646 loop : -0.63 (0.13), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 353 HIS 0.003 0.001 HIS C1064 PHE 0.024 0.001 PHE A 238 TYR 0.018 0.001 TYR B 351 ARG 0.009 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 3.533 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 153 MET cc_start: 0.5588 (ptt) cc_final: 0.5205 (ppp) REVERT: A 170 TYR cc_start: 0.8679 (t80) cc_final: 0.8355 (t80) REVERT: B 54 LEU cc_start: 0.9235 (mp) cc_final: 0.8802 (tp) REVERT: B 88 ASP cc_start: 0.8896 (m-30) cc_final: 0.8637 (p0) REVERT: B 153 MET cc_start: 0.5807 (ptt) cc_final: 0.4771 (pmt) REVERT: B 369 TYR cc_start: 0.8425 (t80) cc_final: 0.8159 (t80) REVERT: B 370 ASN cc_start: 0.8946 (m-40) cc_final: 0.7904 (p0) REVERT: B 1002 GLN cc_start: 0.7481 (tm-30) cc_final: 0.7200 (tm-30) REVERT: B 1145 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8079 (tm) REVERT: E 473 TRP cc_start: 0.1476 (m-10) cc_final: 0.1074 (m-10) REVERT: E 474 MET cc_start: 0.1549 (mmm) cc_final: 0.0412 (mmm) REVERT: E 559 ARG cc_start: 0.7420 (ptm-80) cc_final: 0.7154 (ttp-110) outliers start: 31 outliers final: 10 residues processed: 166 average time/residue: 1.3988 time to fit residues: 277.0039 Evaluate side-chains 126 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 265 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 319 optimal weight: 8.9990 chunk 344 optimal weight: 8.9990 chunk 284 optimal weight: 0.6980 chunk 316 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 388 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 824 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS E 524 GLN E 552 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 29241 Z= 0.229 Angle : 0.524 8.838 39787 Z= 0.267 Chirality : 0.043 0.267 4653 Planarity : 0.004 0.041 5070 Dihedral : 4.909 57.006 5105 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.36 % Allowed : 8.71 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.71 (0.14), residues: 3465 helix: 2.07 (0.16), residues: 1029 sheet: 0.53 (0.20), residues: 619 loop : -0.48 (0.13), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 353 HIS 0.003 0.001 HIS E 378 PHE 0.019 0.001 PHE A 168 TYR 0.023 0.001 TYR B 365 ARG 0.007 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 131 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7785 (m-80) cc_final: 0.7151 (m-10) REVERT: A 329 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.7256 (m-10) REVERT: A 1002 GLN cc_start: 0.8418 (tp40) cc_final: 0.8140 (tp40) REVERT: A 1010 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: B 54 LEU cc_start: 0.9242 (mp) cc_final: 0.8749 (tp) REVERT: B 88 ASP cc_start: 0.8886 (m-30) cc_final: 0.8653 (p0) REVERT: B 153 MET cc_start: 0.5945 (ptt) cc_final: 0.4926 (pmt) REVERT: B 369 TYR cc_start: 0.8419 (t80) cc_final: 0.8133 (t80) REVERT: B 370 ASN cc_start: 0.8927 (m-40) cc_final: 0.7892 (p0) REVERT: B 425 LEU cc_start: 0.6256 (mm) cc_final: 0.5931 (mp) REVERT: B 1002 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7467 (tm-30) REVERT: B 1145 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8257 (tm) REVERT: C 130 VAL cc_start: 0.8364 (t) cc_final: 0.8048 (p) REVERT: C 245 HIS cc_start: 0.6384 (OUTLIER) cc_final: 0.5890 (m-70) REVERT: C 434 ILE cc_start: 0.5975 (OUTLIER) cc_final: 0.5751 (pp) REVERT: E 366 MET cc_start: 0.2366 (tpt) cc_final: 0.2107 (tpp) REVERT: E 474 MET cc_start: 0.0729 (mmm) cc_final: 0.0426 (mmm) REVERT: E 559 ARG cc_start: 0.7635 (ptm-80) cc_final: 0.7414 (ttp-110) REVERT: E 613 TYR cc_start: 0.5087 (t80) cc_final: 0.4684 (m-10) outliers start: 42 outliers final: 12 residues processed: 160 average time/residue: 1.1883 time to fit residues: 231.3513 Evaluate side-chains 131 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 40.0000 chunk 240 optimal weight: 7.9990 chunk 165 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 214 optimal weight: 4.9990 chunk 320 optimal weight: 4.9990 chunk 339 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 303 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B 926 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 29241 Z= 0.378 Angle : 0.579 9.774 39787 Z= 0.292 Chirality : 0.045 0.253 4653 Planarity : 0.004 0.038 5070 Dihedral : 5.097 58.762 5105 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.30 % Allowed : 9.46 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.70 (0.14), residues: 3465 helix: 2.17 (0.16), residues: 1016 sheet: 0.32 (0.19), residues: 694 loop : -0.48 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 886 HIS 0.005 0.001 HIS E 265 PHE 0.029 0.002 PHE A 157 TYR 0.030 0.002 TYR B 351 ARG 0.005 0.001 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 119 time to evaluate : 3.593 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 170 TYR cc_start: 0.8705 (t80) cc_final: 0.8455 (t80) REVERT: A 200 TYR cc_start: 0.7925 (m-80) cc_final: 0.7284 (m-10) REVERT: A 329 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.7446 (m-10) REVERT: A 1002 GLN cc_start: 0.8565 (tp-100) cc_final: 0.8266 (tp40) REVERT: B 54 LEU cc_start: 0.9303 (mp) cc_final: 0.8753 (tp) REVERT: B 153 MET cc_start: 0.6250 (ptt) cc_final: 0.5181 (pmt) REVERT: B 369 TYR cc_start: 0.8525 (t80) cc_final: 0.8225 (t80) REVERT: B 370 ASN cc_start: 0.8969 (m-40) cc_final: 0.7955 (p0) REVERT: B 425 LEU cc_start: 0.6303 (mm) cc_final: 0.6002 (mp) REVERT: B 1002 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7464 (tm-30) REVERT: B 1145 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8237 (tm) REVERT: C 130 VAL cc_start: 0.8421 (t) cc_final: 0.8138 (p) REVERT: C 245 HIS cc_start: 0.6361 (OUTLIER) cc_final: 0.5846 (m-70) REVERT: C 434 ILE cc_start: 0.6159 (OUTLIER) cc_final: 0.5906 (pp) REVERT: E 140 GLU cc_start: 0.1129 (OUTLIER) cc_final: 0.0798 (tt0) REVERT: E 358 ILE cc_start: 0.3101 (OUTLIER) cc_final: 0.2809 (tp) REVERT: E 559 ARG cc_start: 0.7600 (ptm-80) cc_final: 0.7364 (ttp-110) REVERT: E 606 TRP cc_start: 0.2241 (p90) cc_final: 0.2020 (p90) REVERT: E 613 TYR cc_start: 0.5005 (t80) cc_final: 0.4645 (m-10) outliers start: 40 outliers final: 13 residues processed: 146 average time/residue: 1.1880 time to fit residues: 213.4543 Evaluate side-chains 129 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 252 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 289 optimal weight: 0.8980 chunk 234 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 173 optimal weight: 0.9980 chunk 304 optimal weight: 0.0070 chunk 85 optimal weight: 0.3980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 926 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29241 Z= 0.143 Angle : 0.491 11.087 39787 Z= 0.247 Chirality : 0.043 0.275 4653 Planarity : 0.003 0.038 5070 Dihedral : 4.760 57.144 5105 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.87 % Allowed : 10.24 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.92 (0.14), residues: 3465 helix: 2.44 (0.16), residues: 1011 sheet: 0.39 (0.20), residues: 637 loop : -0.34 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 594 HIS 0.003 0.000 HIS E 265 PHE 0.021 0.001 PHE A 157 TYR 0.021 0.001 TYR B 351 ARG 0.007 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 3.194 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 170 TYR cc_start: 0.8745 (t80) cc_final: 0.8496 (t80) REVERT: A 200 TYR cc_start: 0.7959 (m-80) cc_final: 0.7314 (m-10) REVERT: A 1002 GLN cc_start: 0.8488 (tp-100) cc_final: 0.8137 (tp40) REVERT: B 54 LEU cc_start: 0.9191 (mp) cc_final: 0.8733 (tp) REVERT: B 153 MET cc_start: 0.6210 (ptt) cc_final: 0.5268 (pmt) REVERT: B 369 TYR cc_start: 0.8497 (t80) cc_final: 0.8203 (t80) REVERT: B 370 ASN cc_start: 0.8956 (m-40) cc_final: 0.7922 (p0) REVERT: B 425 LEU cc_start: 0.6277 (mm) cc_final: 0.5997 (mp) REVERT: B 1002 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7337 (tm-30) REVERT: C 130 VAL cc_start: 0.8410 (t) cc_final: 0.8133 (p) REVERT: C 245 HIS cc_start: 0.6398 (OUTLIER) cc_final: 0.5912 (m-70) REVERT: C 434 ILE cc_start: 0.6110 (OUTLIER) cc_final: 0.5865 (pp) REVERT: E 358 ILE cc_start: 0.3865 (OUTLIER) cc_final: 0.3506 (tt) REVERT: E 559 ARG cc_start: 0.7699 (ptm-80) cc_final: 0.7472 (ttp-110) REVERT: E 606 TRP cc_start: 0.2354 (p90) cc_final: 0.2120 (p90) REVERT: E 613 TYR cc_start: 0.4902 (t80) cc_final: 0.4550 (m-10) outliers start: 27 outliers final: 12 residues processed: 137 average time/residue: 1.2066 time to fit residues: 201.6843 Evaluate side-chains 126 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 114 optimal weight: 0.2980 chunk 305 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 339 optimal weight: 7.9990 chunk 281 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29241 Z= 0.191 Angle : 0.486 9.587 39787 Z= 0.245 Chirality : 0.043 0.269 4653 Planarity : 0.003 0.036 5070 Dihedral : 4.667 57.620 5105 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.00 % Allowed : 10.46 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.99 (0.14), residues: 3465 helix: 2.52 (0.16), residues: 1011 sheet: 0.33 (0.20), residues: 669 loop : -0.28 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 594 HIS 0.003 0.001 HIS E 265 PHE 0.018 0.001 PHE A 157 TYR 0.018 0.001 TYR B 351 ARG 0.005 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 117 time to evaluate : 3.143 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 170 TYR cc_start: 0.8753 (t80) cc_final: 0.8496 (t80) REVERT: A 200 TYR cc_start: 0.8092 (m-80) cc_final: 0.7537 (m-10) REVERT: A 1002 GLN cc_start: 0.8528 (tp-100) cc_final: 0.8167 (tp40) REVERT: B 54 LEU cc_start: 0.9228 (mp) cc_final: 0.8783 (tp) REVERT: B 153 MET cc_start: 0.6203 (ptt) cc_final: 0.5145 (pmt) REVERT: B 369 TYR cc_start: 0.8502 (t80) cc_final: 0.8219 (t80) REVERT: B 370 ASN cc_start: 0.8972 (m-40) cc_final: 0.7955 (p0) REVERT: B 425 LEU cc_start: 0.6234 (mm) cc_final: 0.5937 (mp) REVERT: B 1002 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7340 (tm-30) REVERT: C 130 VAL cc_start: 0.8443 (t) cc_final: 0.8149 (p) REVERT: C 245 HIS cc_start: 0.6389 (OUTLIER) cc_final: 0.5878 (m-70) REVERT: C 434 ILE cc_start: 0.6164 (OUTLIER) cc_final: 0.5927 (pp) REVERT: E 140 GLU cc_start: 0.1063 (OUTLIER) cc_final: 0.0612 (mt-10) REVERT: E 358 ILE cc_start: 0.3465 (OUTLIER) cc_final: 0.3069 (tt) REVERT: E 606 TRP cc_start: 0.2322 (p90) cc_final: 0.2103 (p90) REVERT: E 613 TYR cc_start: 0.4941 (t80) cc_final: 0.4593 (m-10) outliers start: 31 outliers final: 14 residues processed: 138 average time/residue: 1.1931 time to fit residues: 201.0704 Evaluate side-chains 125 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 338 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 501 ASN B 926 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 29241 Z= 0.428 Angle : 0.599 10.143 39787 Z= 0.302 Chirality : 0.045 0.247 4653 Planarity : 0.004 0.059 5070 Dihedral : 5.164 59.670 5105 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.23 % Allowed : 10.50 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.76 (0.14), residues: 3465 helix: 2.31 (0.16), residues: 1011 sheet: 0.05 (0.19), residues: 719 loop : -0.36 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 353 HIS 0.004 0.001 HIS C1064 PHE 0.024 0.002 PHE C 106 TYR 0.022 0.002 TYR A 904 ARG 0.011 0.001 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 109 time to evaluate : 3.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8263 (m-80) cc_final: 0.8017 (m-80) REVERT: A 1002 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8292 (tp40) REVERT: B 153 MET cc_start: 0.6158 (ptt) cc_final: 0.5321 (pmt) REVERT: B 369 TYR cc_start: 0.8575 (t80) cc_final: 0.8278 (t80) REVERT: B 370 ASN cc_start: 0.9000 (m-40) cc_final: 0.8000 (p0) REVERT: B 425 LEU cc_start: 0.6267 (mm) cc_final: 0.5955 (mp) REVERT: B 1002 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7346 (tm-30) REVERT: B 1146 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7368 (t0) REVERT: C 130 VAL cc_start: 0.8431 (t) cc_final: 0.8107 (p) REVERT: C 245 HIS cc_start: 0.6423 (OUTLIER) cc_final: 0.6017 (m-70) REVERT: C 434 ILE cc_start: 0.6233 (OUTLIER) cc_final: 0.6009 (pp) REVERT: E 606 TRP cc_start: 0.2371 (p90) cc_final: 0.2166 (p90) REVERT: E 613 TYR cc_start: 0.4977 (t80) cc_final: 0.4649 (m-10) outliers start: 38 outliers final: 17 residues processed: 136 average time/residue: 1.1054 time to fit residues: 186.4092 Evaluate side-chains 124 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 209 optimal weight: 30.0000 chunk 135 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 215 optimal weight: 0.3980 chunk 230 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 31 optimal weight: 0.0670 chunk 265 optimal weight: 0.7980 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29241 Z= 0.196 Angle : 0.506 9.695 39787 Z= 0.256 Chirality : 0.043 0.333 4653 Planarity : 0.003 0.037 5070 Dihedral : 4.949 58.252 5105 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.84 % Allowed : 11.18 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.89 (0.14), residues: 3465 helix: 2.51 (0.16), residues: 1010 sheet: 0.03 (0.19), residues: 696 loop : -0.28 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 353 HIS 0.003 0.001 HIS E 493 PHE 0.016 0.001 PHE A 157 TYR 0.030 0.001 TYR E 497 ARG 0.006 0.000 ARG E 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 110 time to evaluate : 3.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.8563 (tp-100) cc_final: 0.8186 (tp40) REVERT: B 153 MET cc_start: 0.6144 (ptt) cc_final: 0.5293 (pmt) REVERT: B 369 TYR cc_start: 0.8528 (t80) cc_final: 0.8226 (t80) REVERT: B 370 ASN cc_start: 0.9018 (m-40) cc_final: 0.8041 (p0) REVERT: B 425 LEU cc_start: 0.6246 (mm) cc_final: 0.5952 (mp) REVERT: B 740 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7808 (tpt) REVERT: B 1002 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7263 (tm-30) REVERT: C 130 VAL cc_start: 0.8379 (t) cc_final: 0.8068 (p) REVERT: C 245 HIS cc_start: 0.6389 (OUTLIER) cc_final: 0.5971 (m-70) REVERT: C 434 ILE cc_start: 0.6223 (OUTLIER) cc_final: 0.6007 (pp) REVERT: E 613 TYR cc_start: 0.4935 (t80) cc_final: 0.4599 (m-10) outliers start: 26 outliers final: 12 residues processed: 127 average time/residue: 1.2924 time to fit residues: 200.1407 Evaluate side-chains 115 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 307 optimal weight: 10.0000 chunk 324 optimal weight: 1.9990 chunk 295 optimal weight: 10.0000 chunk 315 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 284 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 chunk 314 optimal weight: 30.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 29241 Z= 0.350 Angle : 0.561 9.273 39787 Z= 0.284 Chirality : 0.045 0.371 4653 Planarity : 0.004 0.038 5070 Dihedral : 5.095 59.158 5105 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.78 % Allowed : 11.50 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.80 (0.14), residues: 3465 helix: 2.41 (0.16), residues: 1018 sheet: -0.04 (0.19), residues: 719 loop : -0.31 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 594 HIS 0.004 0.001 HIS E 493 PHE 0.020 0.001 PHE C 338 TYR 0.029 0.001 TYR A 170 ARG 0.006 0.000 ARG E 559 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5712 (ptt) cc_final: 0.5223 (ppp) REVERT: A 1002 GLN cc_start: 0.8649 (tp-100) cc_final: 0.8283 (tp40) REVERT: B 153 MET cc_start: 0.6226 (ptt) cc_final: 0.5171 (pmt) REVERT: B 369 TYR cc_start: 0.8571 (t80) cc_final: 0.8279 (t80) REVERT: B 370 ASN cc_start: 0.8970 (m-40) cc_final: 0.7932 (p0) REVERT: B 425 LEU cc_start: 0.6229 (mm) cc_final: 0.5920 (mp) REVERT: B 1002 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7328 (tm-30) REVERT: C 130 VAL cc_start: 0.8413 (t) cc_final: 0.8099 (p) REVERT: C 245 HIS cc_start: 0.6509 (OUTLIER) cc_final: 0.6076 (m-70) REVERT: C 434 ILE cc_start: 0.6278 (OUTLIER) cc_final: 0.6055 (pp) REVERT: E 376 MET cc_start: 0.2050 (mmp) cc_final: 0.1359 (mpp) REVERT: E 613 TYR cc_start: 0.4976 (t80) cc_final: 0.4629 (m-10) outliers start: 24 outliers final: 14 residues processed: 119 average time/residue: 1.2494 time to fit residues: 181.9200 Evaluate side-chains 117 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 207 optimal weight: 0.0980 chunk 333 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 231 optimal weight: 50.0000 chunk 349 optimal weight: 20.0000 chunk 321 optimal weight: 20.0000 chunk 278 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 215 optimal weight: 0.0570 chunk 170 optimal weight: 6.9990 overall best weight: 1.0304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29241 Z= 0.181 Angle : 0.514 10.163 39787 Z= 0.260 Chirality : 0.044 0.366 4653 Planarity : 0.003 0.040 5070 Dihedral : 4.915 58.165 5105 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.75 % Allowed : 11.56 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.93 (0.14), residues: 3465 helix: 2.53 (0.16), residues: 1016 sheet: -0.02 (0.20), residues: 668 loop : -0.22 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 353 HIS 0.004 0.001 HIS E 493 PHE 0.016 0.001 PHE B 456 TYR 0.016 0.001 TYR B 351 ARG 0.006 0.000 ARG E 559 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5708 (ptt) cc_final: 0.5264 (ppp) REVERT: A 1002 GLN cc_start: 0.8559 (tp-100) cc_final: 0.8174 (tp40) REVERT: B 153 MET cc_start: 0.6137 (ptt) cc_final: 0.5159 (pmt) REVERT: B 369 TYR cc_start: 0.8545 (t80) cc_final: 0.8254 (t80) REVERT: B 370 ASN cc_start: 0.8958 (m-40) cc_final: 0.7907 (p0) REVERT: B 425 LEU cc_start: 0.6237 (mm) cc_final: 0.5935 (mp) REVERT: B 740 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7795 (tpt) REVERT: B 1002 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7233 (tm-30) REVERT: C 130 VAL cc_start: 0.8367 (t) cc_final: 0.8064 (p) REVERT: C 173 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: C 434 ILE cc_start: 0.6237 (OUTLIER) cc_final: 0.6034 (pp) REVERT: E 376 MET cc_start: 0.1993 (mmp) cc_final: 0.1458 (mpp) REVERT: E 613 TYR cc_start: 0.5001 (t80) cc_final: 0.4678 (m-10) outliers start: 23 outliers final: 13 residues processed: 117 average time/residue: 1.2335 time to fit residues: 175.5353 Evaluate side-chains 112 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 221 optimal weight: 20.0000 chunk 296 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 286 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.134347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.092827 restraints weight = 102315.856| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 5.28 r_work: 0.2975 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 29241 Z= 0.307 Angle : 0.555 12.655 39787 Z= 0.280 Chirality : 0.045 0.355 4653 Planarity : 0.003 0.040 5070 Dihedral : 5.039 58.929 5105 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.71 % Allowed : 11.66 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.87 (0.14), residues: 3465 helix: 2.46 (0.16), residues: 1025 sheet: -0.02 (0.19), residues: 700 loop : -0.28 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 594 HIS 0.005 0.001 HIS E 493 PHE 0.020 0.001 PHE A 106 TYR 0.034 0.001 TYR A 170 ARG 0.006 0.000 ARG E 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8045.64 seconds wall clock time: 145 minutes 45.73 seconds (8745.73 seconds total)