Starting phenix.real_space_refine on Sun Mar 24 05:26:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v82_31787/03_2024/7v82_31787.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v82_31787/03_2024/7v82_31787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v82_31787/03_2024/7v82_31787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v82_31787/03_2024/7v82_31787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v82_31787/03_2024/7v82_31787.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v82_31787/03_2024/7v82_31787.pdb" } resolution = 2.8 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= -0.002 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 198 5.16 5 C 25566 2.51 5 N 6525 2.21 5 O 7803 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 GLU 661": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 536": "OE1" <-> "OE2" Residue "F TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 597": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40092 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "B" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "C" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} 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: {'PTRANS': 27, 'TRANS': 568} Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" 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: "Z" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 19.98, per 1000 atoms: 0.50 Number of scatterers: 40092 At special positions: 0 Unit cell: (167.2, 181.5, 242, 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 198 16.00 O 7803 8.00 N 6525 7.00 C 25566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 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=2.03 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=2.04 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 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=2.04 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.02 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 234 " " NAG A2005 " - " ASN A 603 " " NAG A2006 " - " ASN A 657 " " NAG A2007 " - " ASN A 20 " " NAG A2008 " - " ASN A 188 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 165 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 343 " " NAG B2005 " - " ASN B 603 " " NAG B2006 " - " ASN B 657 " " NAG B2007 " - " ASN B 20 " " NAG B2008 " - " ASN B 188 " " NAG C2001 " - " ASN C 61 " " NAG C2003 " - " ASN C 165 " " NAG C2004 " - " ASN C 234 " " NAG C2005 " - " ASN C 343 " " NAG C2006 " - " ASN C 603 " " NAG C2007 " - " ASN C 657 " " NAG C2008 " - " ASN C 20 " " NAG C2009 " - " ASN C 188 " " NAG D1001 " - " ASN D 53 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 331 " " NAG I 1 " - " ASN A 343 " " NAG J 1 " - " ASN A 616 " " NAG K 1 " - " ASN A 709 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 282 " " NAG S 1 " - " ASN B 331 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 709 " " NAG V 1 " - " ASN B 717 " " NAG W 1 " - " ASN B 801 " " NAG X 1 " - " ASN B1074 " " NAG Y 1 " - " ASN B1098 " " NAG Z 1 " - " ASN B1134 " " NAG a 1 " - " ASN C 282 " " NAG b 1 " - " ASN C 331 " " NAG d 1 " - " ASN C 709 " " NAG e 1 " - " ASN C 717 " " NAG f 1 " - " ASN C 801 " " NAG g 1 " - " ASN C1074 " " NAG h 1 " - " ASN C1098 " " NAG i 1 " - " ASN C1134 " Time building additional restraints: 16.24 Conformation dependent library (CDL) restraints added in 6.6 seconds 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9210 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 51 sheets defined 37.9% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.343A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.064A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.059A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.513A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.688A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.541A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.788A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.550A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.657A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.652A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.686A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.786A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.166A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.611A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.943A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.965A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (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 886 through 890 Processing helix chain 'B' and resid 898 through 908 removed outlier: 3.592A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.247A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (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 982 removed outlier: 3.550A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.287A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.905A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.534A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.519A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.042A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.557A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.606A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.720A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.432A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.072A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 53 removed outlier: 3.519A pdb=" N LYS E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 58 through 80 removed outlier: 4.230A pdb=" N MET E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN E 76 " --> pdb=" O PHE E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.627A pdb=" N LEU E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 Processing helix chain 'E' and resid 147 through 152 removed outlier: 3.910A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 172 removed outlier: 3.647A pdb=" N VAL E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 194 removed outlier: 3.671A pdb=" N TYR E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 218 through 224 removed outlier: 3.921A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 218 through 224' Processing helix chain 'E' and resid 234 through 252 removed outlier: 3.708A pdb=" N GLU E 238 " --> pdb=" O LYS E 234 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.601A pdb=" N LYS E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE E 314 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE E 315 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.810A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 398 through 413 removed outlier: 4.268A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.688A pdb=" N ILE E 421 " --> pdb=" O HIS E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.621A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 474 through 485 Processing helix chain 'E' and resid 503 through 507 removed outlier: 3.704A pdb=" N VAL E 506 " --> pdb=" O LEU E 503 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER E 507 " --> pdb=" O PHE E 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 503 through 507' Processing helix chain 'E' and resid 513 through 532 removed outlier: 4.180A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.661A pdb=" N LYS E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 564 removed outlier: 3.640A pdb=" N GLU E 564 " --> pdb=" O GLY E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 570 Processing helix chain 'E' and resid 582 through 588 removed outlier: 3.777A pdb=" N ASN E 586 " --> pdb=" O ARG E 582 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 597 removed outlier: 3.591A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.541A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.928A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN D 76 " --> pdb=" O PHE D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.573A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 128 Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 158 through 171 Processing helix chain 'D' and resid 175 through 194 removed outlier: 3.960A pdb=" N LEU D 179 " --> pdb=" O GLN D 175 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.677A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 227 removed outlier: 4.035A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 233 through 252 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.581A pdb=" N GLY D 268 " --> pdb=" O HIS D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.091A pdb=" N PHE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.750A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.751A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 413 removed outlier: 3.603A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.525A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 473 through 485 Processing helix chain 'D' and resid 503 through 507 removed outlier: 3.884A pdb=" N SER D 507 " --> pdb=" O PHE D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.695A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.679A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.564A pdb=" N SER D 563 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU D 564 " --> pdb=" O GLY D 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 560 through 564' Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 582 through 588 removed outlier: 3.714A pdb=" N ASN D 586 " --> pdb=" O ARG D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 597 removed outlier: 3.505A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 53 removed outlier: 4.293A pdb=" N THR F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 80 removed outlier: 3.808A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 76 " --> pdb=" O PHE F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 109 through 128 removed outlier: 3.572A pdb=" N SER F 128 " --> pdb=" O SER F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 154 removed outlier: 3.755A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 169 removed outlier: 3.715A pdb=" N ALA F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 194 removed outlier: 3.951A pdb=" N LEU F 179 " --> pdb=" O GLN F 175 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 removed outlier: 3.844A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 229 removed outlier: 3.867A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 233 through 252 Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 301 Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.665A pdb=" N LYS F 313 " --> pdb=" O LYS F 309 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE F 314 " --> pdb=" O GLU F 310 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE F 315 " --> pdb=" O ALA F 311 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL F 316 " --> pdb=" O GLU F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 365 through 385 Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.565A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 413 removed outlier: 3.867A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 4.290A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 465 Processing helix chain 'F' and resid 474 through 485 Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.633A pdb=" N VAL F 506 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER F 507 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 507' Processing helix chain 'F' and resid 513 through 532 removed outlier: 3.782A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.713A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN F 552 " --> pdb=" O THR F 548 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG F 559 " --> pdb=" O PHE F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 582 through 588 removed outlier: 3.672A pdb=" N ASN F 586 " --> pdb=" O ARG F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 597 removed outlier: 3.556A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.732A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.454A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.954A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.027A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 573 through 576 removed outlier: 3.984A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.961A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.019A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.452A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.723A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.840A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.058A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.054A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 134 through 135 removed outlier: 3.799A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 143 through 144 removed outlier: 5.360A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.558A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.670A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.567A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.915A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 712 Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.119A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.725A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.042A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.896A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.770A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 11.496A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.431A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.052A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.684A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.941A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AE6, first strand: chain 'C' and resid 717 through 728 removed outlier: 5.991A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.633A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.950A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AF2, first strand: chain 'E' and resid 347 through 350 Processing sheet with id=AF3, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AF4, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.138A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AF6, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.005A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 1670 hydrogen bonds defined for protein. 4686 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: 16.60 Time building geometry restraints manager: 17.64 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: 12688 1.34 - 1.46: 10170 1.46 - 1.58: 17920 1.58 - 1.70: 1 1.70 - 1.83: 288 Bond restraints: 41067 Sorted by residual: bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.43e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.33e+00 bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.18e+00 bond pdb=" CB PRO E 492 " pdb=" CG PRO E 492 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.61e+00 bond pdb=" C1 NAG B2008 " pdb=" O5 NAG B2008 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.26e+00 ... (remaining 41062 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.58: 837 105.58 - 112.69: 21721 112.69 - 119.81: 13253 119.81 - 126.92: 19530 126.92 - 134.04: 519 Bond angle restraints: 55860 Sorted by residual: angle pdb=" C LEU C 984 " pdb=" N ASP C 985 " pdb=" CA ASP C 985 " ideal model delta sigma weight residual 120.67 129.49 -8.82 1.34e+00 5.57e-01 4.34e+01 angle pdb=" CA PRO E 492 " pdb=" N PRO E 492 " pdb=" CD PRO E 492 " ideal model delta sigma weight residual 112.00 104.52 7.48 1.40e+00 5.10e-01 2.85e+01 angle pdb=" C GLU E 375 " pdb=" N MET E 376 " pdb=" CA MET E 376 " ideal model delta sigma weight residual 121.58 114.21 7.37 1.95e+00 2.63e-01 1.43e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 114.04 109.55 4.49 1.24e+00 6.50e-01 1.31e+01 angle pdb=" N ILE F 21 " pdb=" CA ILE F 21 " pdb=" C ILE F 21 " ideal model delta sigma weight residual 113.42 109.28 4.14 1.17e+00 7.31e-01 1.25e+01 ... (remaining 55855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.93: 23900 24.93 - 49.85: 1294 49.85 - 74.78: 156 74.78 - 99.71: 50 99.71 - 124.64: 34 Dihedral angle restraints: 25434 sinusoidal: 11115 harmonic: 14319 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual 93.00 -177.52 -89.48 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 -178.04 -88.96 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 177.81 -84.81 1 1.00e+01 1.00e-02 8.73e+01 ... (remaining 25431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 6077 0.096 - 0.192: 306 0.192 - 0.288: 5 0.288 - 0.385: 5 0.385 - 0.481: 1 Chirality restraints: 6394 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" C1 NAG A2002 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A2002 " pdb=" O5 NAG A2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 6391 not shown) Planarity restraints: 7163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 491 " 0.091 5.00e-02 4.00e+02 1.34e-01 2.86e+01 pdb=" N PRO E 492 " -0.231 5.00e-02 4.00e+02 pdb=" CA PRO E 492 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO E 492 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.030 2.00e-02 2.50e+03 2.79e-02 9.72e+00 pdb=" CG ASN C1074 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.031 2.00e-02 2.50e+03 pdb=" C1 NAG g 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO C 987 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.039 5.00e-02 4.00e+02 ... (remaining 7160 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1169 2.70 - 3.25: 40074 3.25 - 3.80: 63496 3.80 - 4.35: 78915 4.35 - 4.90: 132798 Nonbonded interactions: 316452 Sorted by model distance: nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.150 2.440 nonbonded pdb=" O ASP B 442 " pdb=" ND2 ASN B 448 " model vdw 2.186 2.520 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.192 2.440 nonbonded pdb=" O ILE E 151 " pdb=" OG SER E 155 " model vdw 2.196 2.440 nonbonded pdb=" OD2 ASP B 796 " pdb=" O6 NAG K 1 " model vdw 2.200 2.440 ... (remaining 316447 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 14 through 1146 or resid 2001 through 2008)) } ncs_group { reference = (chain 'D' and resid 19 through 614) selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 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: 0.040 Extract box with map and model: 14.660 Check model and map are aligned: 0.560 Set scattering table: 0.330 Process input model: 102.390 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.590 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 0.107 41067 Z= 0.300 Angle : 0.623 9.273 55860 Z= 0.320 Chirality : 0.046 0.481 6394 Planarity : 0.004 0.134 7110 Dihedral : 15.217 124.636 16080 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.12), residues: 4848 helix: 1.24 (0.14), residues: 1592 sheet: 0.01 (0.18), residues: 747 loop : -1.40 (0.12), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 886 HIS 0.013 0.001 HIS E 373 PHE 0.040 0.001 PHE C 906 TYR 0.021 0.001 TYR A 873 ARG 0.005 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 4.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5302 (ppp) cc_final: 0.5060 (pp-130) REVERT: E 163 TRP cc_start: 0.8195 (m100) cc_final: 0.7553 (t60) REVERT: E 360 MET cc_start: 0.1436 (ptm) cc_final: -0.0109 (tpt) REVERT: E 480 MET cc_start: 0.1033 (mpp) cc_final: 0.0387 (ttp) REVERT: D 366 MET cc_start: 0.5490 (tpt) cc_final: 0.5127 (tpp) REVERT: F 332 MET cc_start: 0.1101 (ppp) cc_final: 0.0296 (pmm) REVERT: F 366 MET cc_start: 0.1461 (tpt) cc_final: 0.1176 (mmm) REVERT: F 462 MET cc_start: 0.6590 (ptm) cc_final: 0.6124 (mmt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 1.5723 time to fit residues: 231.6416 Evaluate side-chains 107 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 4.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 410 optimal weight: 50.0000 chunk 368 optimal weight: 40.0000 chunk 204 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 380 optimal weight: 0.9980 chunk 147 optimal weight: 40.0000 chunk 231 optimal weight: 0.7980 chunk 283 optimal weight: 0.9980 chunk 441 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN D 330 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.0543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41067 Z= 0.207 Angle : 0.555 9.472 55860 Z= 0.279 Chirality : 0.043 0.340 6394 Planarity : 0.004 0.071 7110 Dihedral : 10.265 115.067 7029 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.35 % Allowed : 5.10 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.12), residues: 4848 helix: 1.34 (0.13), residues: 1617 sheet: 0.14 (0.18), residues: 742 loop : -1.36 (0.12), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 886 HIS 0.010 0.001 HIS E 195 PHE 0.021 0.001 PHE C 906 TYR 0.023 0.001 TYR F 385 ARG 0.003 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 4.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5250 (ppp) cc_final: 0.4972 (pp-130) REVERT: C 153 MET cc_start: 0.6864 (tmm) cc_final: 0.6397 (tmm) REVERT: E 163 TRP cc_start: 0.8121 (m100) cc_final: 0.7548 (t60) REVERT: E 360 MET cc_start: 0.1156 (ptm) cc_final: -0.0132 (tpt) REVERT: E 480 MET cc_start: 0.0943 (mpp) cc_final: 0.0315 (ttt) REVERT: D 332 MET cc_start: 0.2010 (pp-130) cc_final: 0.1656 (ppp) REVERT: F 366 MET cc_start: 0.1905 (tpt) cc_final: 0.1557 (mmm) REVERT: F 408 MET cc_start: 0.1506 (ttt) cc_final: 0.1265 (ttt) REVERT: F 462 MET cc_start: 0.6489 (ptm) cc_final: 0.5927 (mmt) REVERT: F 480 MET cc_start: 0.4047 (pp-130) cc_final: 0.2909 (pp-130) outliers start: 15 outliers final: 4 residues processed: 109 average time/residue: 1.6754 time to fit residues: 224.1617 Evaluate side-chains 111 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 249 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 245 optimal weight: 40.0000 chunk 136 optimal weight: 10.0000 chunk 367 optimal weight: 30.0000 chunk 300 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 442 optimal weight: 50.0000 chunk 477 optimal weight: 6.9990 chunk 393 optimal weight: 40.0000 chunk 438 optimal weight: 50.0000 chunk 150 optimal weight: 5.9990 chunk 354 optimal weight: 40.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 926 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 41067 Z= 0.483 Angle : 0.653 11.808 55860 Z= 0.328 Chirality : 0.046 0.347 6394 Planarity : 0.004 0.072 7110 Dihedral : 9.836 118.548 7029 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.65 % Allowed : 9.15 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 4848 helix: 1.21 (0.13), residues: 1607 sheet: -0.02 (0.18), residues: 740 loop : -1.42 (0.12), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 886 HIS 0.008 0.001 HIS A1088 PHE 0.027 0.002 PHE C 906 TYR 0.021 0.001 TYR F 385 ARG 0.008 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 4.049 Fit side-chains revert: symmetry clash REVERT: B 153 MET cc_start: 0.5461 (ppp) cc_final: 0.5001 (pp-130) REVERT: C 153 MET cc_start: 0.7024 (tmm) cc_final: 0.6273 (tmm) REVERT: E 163 TRP cc_start: 0.8127 (m100) cc_final: 0.7497 (t60) REVERT: E 360 MET cc_start: 0.1353 (ptm) cc_final: -0.0017 (tpt) REVERT: E 480 MET cc_start: 0.0650 (mpp) cc_final: 0.0024 (ttt) REVERT: D 323 MET cc_start: 0.6875 (tpp) cc_final: 0.6640 (tmt) REVERT: D 332 MET cc_start: 0.2188 (pp-130) cc_final: 0.1807 (ppp) REVERT: F 366 MET cc_start: 0.1898 (tpt) cc_final: 0.1575 (mmm) REVERT: F 480 MET cc_start: 0.3739 (pp-130) cc_final: 0.3074 (pp-130) outliers start: 28 outliers final: 12 residues processed: 126 average time/residue: 1.4748 time to fit residues: 232.4451 Evaluate side-chains 120 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 4.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 436 optimal weight: 50.0000 chunk 332 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 211 optimal weight: 9.9990 chunk 296 optimal weight: 0.6980 chunk 443 optimal weight: 20.0000 chunk 469 optimal weight: 20.0000 chunk 231 optimal weight: 0.9980 chunk 420 optimal weight: 50.0000 chunk 126 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41067 Z= 0.184 Angle : 0.535 9.440 55860 Z= 0.268 Chirality : 0.043 0.358 6394 Planarity : 0.004 0.071 7110 Dihedral : 8.878 116.497 7029 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.93 % Allowed : 10.36 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.12), residues: 4848 helix: 1.43 (0.13), residues: 1608 sheet: 0.10 (0.19), residues: 733 loop : -1.31 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 610 HIS 0.004 0.001 HIS E 374 PHE 0.015 0.001 PHE B1121 TYR 0.020 0.001 TYR F 385 ARG 0.002 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 109 time to evaluate : 5.253 Fit side-chains revert: symmetry clash REVERT: A 1039 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8384 (ptm160) REVERT: B 108 THR cc_start: 0.7504 (OUTLIER) cc_final: 0.7263 (m) REVERT: B 153 MET cc_start: 0.5363 (ppp) cc_final: 0.4863 (pp-130) REVERT: C 153 MET cc_start: 0.6947 (tmm) cc_final: 0.5824 (tmm) REVERT: E 163 TRP cc_start: 0.8110 (m100) cc_final: 0.7528 (t60) REVERT: E 360 MET cc_start: 0.1364 (ptm) cc_final: -0.0012 (tpt) REVERT: E 383 MET cc_start: 0.6184 (mpp) cc_final: 0.5862 (mpp) REVERT: E 480 MET cc_start: 0.0648 (mpp) cc_final: 0.0040 (ttt) REVERT: D 332 MET cc_start: 0.2060 (pp-130) cc_final: 0.1633 (ppp) REVERT: F 332 MET cc_start: 0.2167 (OUTLIER) cc_final: 0.1250 (tmm) REVERT: F 408 MET cc_start: 0.1305 (ttt) cc_final: 0.0162 (tpp) REVERT: F 462 MET cc_start: 0.6313 (ptt) cc_final: 0.5419 (mmt) REVERT: F 480 MET cc_start: 0.3827 (pp-130) cc_final: 0.3333 (pp-130) outliers start: 40 outliers final: 14 residues processed: 135 average time/residue: 1.5091 time to fit residues: 254.6115 Evaluate side-chains 126 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 4.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 391 optimal weight: 9.9990 chunk 266 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 349 optimal weight: 50.0000 chunk 193 optimal weight: 2.9990 chunk 400 optimal weight: 6.9990 chunk 324 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 239 optimal weight: 30.0000 chunk 421 optimal weight: 40.0000 chunk 118 optimal weight: 6.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 675 GLN A 703 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.144 41067 Z= 0.536 Angle : 0.666 11.250 55860 Z= 0.335 Chirality : 0.046 0.373 6394 Planarity : 0.004 0.073 7110 Dihedral : 8.849 119.333 7029 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.35 % Allowed : 11.69 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.12), residues: 4848 helix: 1.25 (0.13), residues: 1607 sheet: -0.04 (0.19), residues: 724 loop : -1.39 (0.12), residues: 2517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 886 HIS 0.007 0.001 HIS A1088 PHE 0.025 0.002 PHE A1121 TYR 0.022 0.001 TYR B1067 ARG 0.004 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 111 time to evaluate : 4.101 Fit side-chains revert: symmetry clash REVERT: A 1039 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8170 (ptm160) REVERT: B 153 MET cc_start: 0.5546 (ppp) cc_final: 0.4963 (pp-130) REVERT: B 1039 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8722 (mtp180) REVERT: C 153 MET cc_start: 0.7117 (tmm) cc_final: 0.5938 (tmm) REVERT: E 163 TRP cc_start: 0.8127 (m100) cc_final: 0.7508 (t60) REVERT: E 270 MET cc_start: 0.3385 (tpp) cc_final: 0.2484 (tmt) REVERT: E 360 MET cc_start: 0.1475 (ptm) cc_final: 0.0035 (tpt) REVERT: E 383 MET cc_start: 0.6333 (mpp) cc_final: 0.6072 (mpp) REVERT: E 480 MET cc_start: 0.0440 (mpp) cc_final: -0.0065 (ttt) REVERT: D 323 MET cc_start: 0.6274 (tmt) cc_final: 0.6018 (tmt) REVERT: D 332 MET cc_start: 0.1900 (pp-130) cc_final: 0.1587 (ppp) REVERT: D 455 MET cc_start: 0.4014 (OUTLIER) cc_final: 0.3789 (pp-130) REVERT: D 480 MET cc_start: 0.3173 (OUTLIER) cc_final: 0.2489 (pp-130) REVERT: F 332 MET cc_start: 0.2452 (OUTLIER) cc_final: 0.1555 (tmm) REVERT: F 408 MET cc_start: 0.1349 (ttt) cc_final: 0.1121 (ttt) REVERT: F 480 MET cc_start: 0.3898 (pp-130) cc_final: 0.3641 (pp-130) outliers start: 58 outliers final: 26 residues processed: 155 average time/residue: 1.3868 time to fit residues: 271.6203 Evaluate side-chains 141 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 4.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 158 optimal weight: 5.9990 chunk 423 optimal weight: 0.1980 chunk 92 optimal weight: 0.7980 chunk 275 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 470 optimal weight: 50.0000 chunk 390 optimal weight: 50.0000 chunk 217 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 155 optimal weight: 7.9990 chunk 246 optimal weight: 30.0000 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 ASN F 493 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 41067 Z= 0.322 Angle : 0.582 12.200 55860 Z= 0.291 Chirality : 0.044 0.366 6394 Planarity : 0.004 0.073 7110 Dihedral : 8.375 118.031 7029 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.40 % Allowed : 12.76 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4848 helix: 1.37 (0.13), residues: 1606 sheet: -0.06 (0.19), residues: 719 loop : -1.33 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 886 HIS 0.006 0.001 HIS D 374 PHE 0.019 0.001 PHE A1121 TYR 0.018 0.001 TYR B1067 ARG 0.004 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 110 time to evaluate : 4.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1039 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8479 (ptm160) REVERT: B 153 MET cc_start: 0.5512 (ppp) cc_final: 0.4879 (pp-130) REVERT: B 1039 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8781 (mtp180) REVERT: C 153 MET cc_start: 0.7131 (tmm) cc_final: 0.5918 (tmm) REVERT: E 163 TRP cc_start: 0.8119 (m100) cc_final: 0.7500 (t60) REVERT: E 360 MET cc_start: 0.1469 (ptm) cc_final: 0.0028 (tpt) REVERT: E 480 MET cc_start: 0.0387 (mpp) cc_final: -0.0181 (ttp) REVERT: E 579 MET cc_start: -0.0839 (mmt) cc_final: -0.2232 (mtt) REVERT: E 610 TRP cc_start: 0.3001 (OUTLIER) cc_final: 0.2716 (p-90) REVERT: D 323 MET cc_start: 0.6253 (tmt) cc_final: 0.5935 (tmt) REVERT: D 332 MET cc_start: 0.2034 (pp-130) cc_final: 0.1684 (ppp) REVERT: D 455 MET cc_start: 0.4020 (OUTLIER) cc_final: 0.3793 (pp-130) REVERT: D 480 MET cc_start: 0.3177 (ppp) cc_final: 0.2481 (pp-130) REVERT: F 332 MET cc_start: 0.2271 (OUTLIER) cc_final: 0.1319 (tmm) REVERT: F 408 MET cc_start: 0.1361 (ttt) cc_final: 0.1076 (ttt) REVERT: F 480 MET cc_start: 0.3998 (pp-130) cc_final: 0.3711 (pp-130) outliers start: 60 outliers final: 30 residues processed: 156 average time/residue: 1.4094 time to fit residues: 275.7719 Evaluate side-chains 144 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 109 time to evaluate : 4.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 453 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 343 optimal weight: 20.0000 chunk 266 optimal weight: 0.9990 chunk 395 optimal weight: 10.0000 chunk 262 optimal weight: 0.9990 chunk 468 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 285 optimal weight: 0.9980 chunk 216 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 955 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41067 Z= 0.202 Angle : 0.549 12.103 55860 Z= 0.272 Chirality : 0.043 0.357 6394 Planarity : 0.004 0.071 7110 Dihedral : 7.901 115.806 7029 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.30 % Allowed : 13.04 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.12), residues: 4848 helix: 1.46 (0.13), residues: 1607 sheet: 0.06 (0.19), residues: 733 loop : -1.28 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 349 HIS 0.005 0.001 HIS E 374 PHE 0.015 0.001 PHE B1121 TYR 0.018 0.001 TYR F 385 ARG 0.003 0.000 ARG F 245 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 112 time to evaluate : 4.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1039 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8374 (ptm160) REVERT: B 153 MET cc_start: 0.5476 (ppp) cc_final: 0.4902 (pp-130) REVERT: C 153 MET cc_start: 0.7023 (tmm) cc_final: 0.5784 (tmm) REVERT: E 163 TRP cc_start: 0.8106 (m100) cc_final: 0.7484 (t60) REVERT: E 360 MET cc_start: 0.1473 (ptm) cc_final: 0.0153 (tpt) REVERT: E 371 THR cc_start: 0.0291 (OUTLIER) cc_final: -0.0003 (m) REVERT: E 480 MET cc_start: 0.0429 (mpp) cc_final: -0.0102 (ttt) REVERT: E 579 MET cc_start: -0.0553 (mmt) cc_final: -0.2264 (mtt) REVERT: E 610 TRP cc_start: 0.3337 (OUTLIER) cc_final: 0.3042 (p-90) REVERT: D 224 GLU cc_start: 0.8904 (mp0) cc_final: 0.8596 (pp20) REVERT: D 270 MET cc_start: 0.3567 (tpp) cc_final: 0.3300 (tpp) REVERT: D 323 MET cc_start: 0.6345 (tmt) cc_final: 0.5921 (tmt) REVERT: D 332 MET cc_start: 0.1971 (pp-130) cc_final: 0.1626 (ppp) REVERT: D 455 MET cc_start: 0.4021 (OUTLIER) cc_final: 0.3798 (pp-130) REVERT: D 480 MET cc_start: 0.2943 (OUTLIER) cc_final: 0.2252 (pp-130) REVERT: F 332 MET cc_start: 0.2015 (OUTLIER) cc_final: 0.0043 (ppp) REVERT: F 408 MET cc_start: 0.1271 (ttt) cc_final: 0.0155 (tpp) REVERT: F 462 MET cc_start: 0.5562 (ptt) cc_final: 0.4715 (mmt) REVERT: F 480 MET cc_start: 0.4175 (pp-130) cc_final: 0.3809 (pp-130) outliers start: 56 outliers final: 27 residues processed: 152 average time/residue: 1.4321 time to fit residues: 274.3363 Evaluate side-chains 144 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 289 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 297 optimal weight: 4.9990 chunk 319 optimal weight: 50.0000 chunk 231 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 368 optimal weight: 30.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 955 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 41067 Z= 0.337 Angle : 0.593 11.046 55860 Z= 0.296 Chirality : 0.044 0.361 6394 Planarity : 0.004 0.071 7110 Dihedral : 7.722 115.185 7029 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.63 % Allowed : 13.24 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 4848 helix: 1.40 (0.13), residues: 1609 sheet: 0.04 (0.19), residues: 733 loop : -1.28 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 886 HIS 0.005 0.001 HIS E 374 PHE 0.019 0.001 PHE A1121 TYR 0.019 0.001 TYR B1067 ARG 0.003 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 111 time to evaluate : 4.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1039 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8515 (ptm160) REVERT: B 153 MET cc_start: 0.5681 (ppp) cc_final: 0.5093 (pp-130) REVERT: B 1039 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8776 (mtp180) REVERT: C 153 MET cc_start: 0.7088 (tmm) cc_final: 0.5949 (tmm) REVERT: E 163 TRP cc_start: 0.8095 (m100) cc_final: 0.7536 (t60) REVERT: E 360 MET cc_start: 0.1502 (ptm) cc_final: 0.0171 (tpt) REVERT: E 371 THR cc_start: 0.0297 (OUTLIER) cc_final: -0.0007 (m) REVERT: E 480 MET cc_start: 0.0337 (mpp) cc_final: -0.0210 (ttp) REVERT: E 579 MET cc_start: -0.0391 (mmt) cc_final: -0.2099 (mtt) REVERT: E 610 TRP cc_start: 0.3405 (OUTLIER) cc_final: 0.3094 (p-90) REVERT: D 224 GLU cc_start: 0.8901 (mp0) cc_final: 0.8595 (pp20) REVERT: D 270 MET cc_start: 0.3781 (tpp) cc_final: 0.3503 (tpp) REVERT: D 323 MET cc_start: 0.6339 (tmt) cc_final: 0.5899 (tmt) REVERT: D 332 MET cc_start: 0.2073 (pp-130) cc_final: 0.1702 (ppp) REVERT: D 455 MET cc_start: 0.3965 (OUTLIER) cc_final: 0.3727 (pp-130) REVERT: D 480 MET cc_start: 0.2977 (OUTLIER) cc_final: 0.2272 (pp-130) REVERT: F 332 MET cc_start: 0.1996 (OUTLIER) cc_final: 0.1136 (tmm) REVERT: F 408 MET cc_start: 0.1264 (ttt) cc_final: 0.0118 (tpp) REVERT: F 462 MET cc_start: 0.5671 (ptt) cc_final: 0.4857 (mmt) REVERT: F 480 MET cc_start: 0.4184 (pp-130) cc_final: 0.3811 (pp-130) outliers start: 70 outliers final: 36 residues processed: 165 average time/residue: 1.3150 time to fit residues: 275.4964 Evaluate side-chains 154 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 111 time to evaluate : 4.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 426 optimal weight: 4.9990 chunk 448 optimal weight: 50.0000 chunk 409 optimal weight: 40.0000 chunk 436 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 342 optimal weight: 10.0000 chunk 133 optimal weight: 30.0000 chunk 394 optimal weight: 50.0000 chunk 412 optimal weight: 30.0000 chunk 434 optimal weight: 50.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN B 134 GLN C 360 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 GLN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.149 41067 Z= 0.549 Angle : 0.698 11.673 55860 Z= 0.349 Chirality : 0.047 0.378 6394 Planarity : 0.004 0.075 7110 Dihedral : 7.838 117.093 7029 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.58 % Allowed : 13.66 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.12), residues: 4848 helix: 1.17 (0.13), residues: 1640 sheet: -0.14 (0.19), residues: 702 loop : -1.41 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.007 0.001 HIS A1088 PHE 0.027 0.002 PHE A1121 TYR 0.022 0.001 TYR B1067 ARG 0.004 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 110 time to evaluate : 4.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5722 (ppp) cc_final: 0.5107 (pp-130) REVERT: B 1039 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8746 (mtp180) REVERT: C 153 MET cc_start: 0.7186 (tmm) cc_final: 0.6171 (tmm) REVERT: E 163 TRP cc_start: 0.8097 (m100) cc_final: 0.7533 (t60) REVERT: E 360 MET cc_start: 0.1581 (ptm) cc_final: 0.0208 (tpt) REVERT: E 371 THR cc_start: 0.0412 (OUTLIER) cc_final: 0.0111 (m) REVERT: E 480 MET cc_start: 0.0484 (mpp) cc_final: -0.0001 (ttt) REVERT: E 610 TRP cc_start: 0.3578 (OUTLIER) cc_final: 0.3243 (p-90) REVERT: D 270 MET cc_start: 0.3926 (tpp) cc_final: 0.3545 (tpp) REVERT: D 323 MET cc_start: 0.6439 (tmt) cc_final: 0.6055 (tmt) REVERT: D 332 MET cc_start: 0.1991 (pp-130) cc_final: 0.1632 (ppp) REVERT: D 455 MET cc_start: 0.3962 (OUTLIER) cc_final: 0.3697 (pp-130) REVERT: D 480 MET cc_start: 0.2945 (OUTLIER) cc_final: 0.2216 (pp-130) REVERT: F 332 MET cc_start: 0.2224 (OUTLIER) cc_final: 0.1493 (tmm) REVERT: F 408 MET cc_start: 0.1305 (ttt) cc_final: 0.0123 (tpp) REVERT: F 462 MET cc_start: 0.5432 (ptt) cc_final: 0.4702 (mmt) REVERT: F 480 MET cc_start: 0.4244 (pp-130) cc_final: 0.3875 (pp-130) outliers start: 68 outliers final: 42 residues processed: 163 average time/residue: 1.3735 time to fit residues: 284.8760 Evaluate side-chains 155 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 107 time to evaluate : 4.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 286 optimal weight: 3.9990 chunk 461 optimal weight: 10.0000 chunk 281 optimal weight: 0.1980 chunk 218 optimal weight: 6.9990 chunk 320 optimal weight: 0.2980 chunk 484 optimal weight: 2.9990 chunk 445 optimal weight: 3.9990 chunk 385 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 297 optimal weight: 0.9980 chunk 236 optimal weight: 20.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 955 ASN B 134 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 41067 Z= 0.200 Angle : 0.582 15.071 55860 Z= 0.288 Chirality : 0.043 0.373 6394 Planarity : 0.004 0.072 7110 Dihedral : 7.271 112.383 7029 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.19 % Allowed : 14.06 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.12), residues: 4848 helix: 1.38 (0.13), residues: 1641 sheet: 0.04 (0.19), residues: 726 loop : -1.30 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 165 HIS 0.006 0.001 HIS E 374 PHE 0.015 0.001 PHE B1121 TYR 0.017 0.001 TYR F 385 ARG 0.003 0.000 ARG B1039 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 113 time to evaluate : 4.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1039 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8433 (ptm160) REVERT: B 153 MET cc_start: 0.5570 (ppp) cc_final: 0.5108 (ppp) REVERT: C 153 MET cc_start: 0.6916 (tmm) cc_final: 0.5760 (tmm) REVERT: E 163 TRP cc_start: 0.8096 (m100) cc_final: 0.7538 (t60) REVERT: E 360 MET cc_start: 0.1527 (ptm) cc_final: 0.0183 (tpt) REVERT: E 371 THR cc_start: 0.0611 (OUTLIER) cc_final: 0.0319 (m) REVERT: E 383 MET cc_start: 0.6738 (mpp) cc_final: 0.5579 (pmm) REVERT: E 480 MET cc_start: 0.0461 (mpp) cc_final: -0.0003 (ttt) REVERT: E 579 MET cc_start: -0.0272 (mmt) cc_final: -0.1198 (mtt) REVERT: E 610 TRP cc_start: 0.3559 (OUTLIER) cc_final: 0.3227 (p-90) REVERT: D 224 GLU cc_start: 0.8904 (mp0) cc_final: 0.8594 (pp20) REVERT: D 270 MET cc_start: 0.4212 (tpp) cc_final: 0.3899 (tpp) REVERT: D 323 MET cc_start: 0.6371 (tmt) cc_final: 0.6034 (tmt) REVERT: D 366 MET cc_start: 0.4935 (tpt) cc_final: 0.4729 (tpp) REVERT: D 455 MET cc_start: 0.3955 (OUTLIER) cc_final: 0.3717 (pp-130) REVERT: D 480 MET cc_start: 0.2919 (ppp) cc_final: 0.2252 (pp-130) REVERT: F 332 MET cc_start: 0.1977 (OUTLIER) cc_final: 0.1188 (tmm) REVERT: F 408 MET cc_start: 0.1264 (ttt) cc_final: 0.0137 (tpp) REVERT: F 462 MET cc_start: 0.5398 (ptt) cc_final: 0.4736 (mmt) REVERT: F 480 MET cc_start: 0.4203 (pp-130) cc_final: 0.3890 (pp-130) outliers start: 51 outliers final: 32 residues processed: 151 average time/residue: 1.4646 time to fit residues: 276.9716 Evaluate side-chains 148 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 111 time to evaluate : 4.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 306 optimal weight: 0.7980 chunk 410 optimal weight: 40.0000 chunk 118 optimal weight: 5.9990 chunk 355 optimal weight: 40.0000 chunk 56 optimal weight: 0.0170 chunk 107 optimal weight: 1.9990 chunk 386 optimal weight: 20.0000 chunk 161 optimal weight: 0.9980 chunk 396 optimal weight: 40.0000 chunk 48 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN B 134 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 ASN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.123668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.079518 restraints weight = 182548.492| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 8.45 r_work: 0.2931 rms_B_bonded: 5.21 restraints_weight: 2.0000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 41067 Z= 0.151 Angle : 0.568 21.710 55860 Z= 0.279 Chirality : 0.043 0.358 6394 Planarity : 0.004 0.070 7110 Dihedral : 6.674 103.948 7029 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.19 % Allowed : 14.25 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.12), residues: 4848 helix: 1.53 (0.13), residues: 1646 sheet: 0.16 (0.19), residues: 730 loop : -1.23 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 477 HIS 0.005 0.001 HIS E 374 PHE 0.013 0.001 PHE B1121 TYR 0.017 0.001 TYR F 385 ARG 0.004 0.000 ARG D 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10031.33 seconds wall clock time: 189 minutes 50.61 seconds (11390.61 seconds total)