Starting phenix.real_space_refine on Mon Feb 19 16:25:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7s_31780/02_2024/7v7s_31780.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7s_31780/02_2024/7v7s_31780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7s_31780/02_2024/7v7s_31780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7s_31780/02_2024/7v7s_31780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7s_31780/02_2024/7v7s_31780.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7s_31780/02_2024/7v7s_31780.pdb" } resolution = 3.0 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= 0.038 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 108 5.16 5 C 16039 2.51 5 N 4113 2.21 5 O 4995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A ASP 865": "OD1" <-> "OD2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 426": "OD1" <-> "OD2" Residue "B PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 652": "OE1" <-> "OE2" Residue "C TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "C GLU 771": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25255 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8028 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 53, 'TRANS': 974} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 13.30, per 1000 atoms: 0.53 Number of scatterers: 25255 At special positions: 0 Unit cell: (140.8, 145.2, 199.1, 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 108 16.00 O 4995 8.00 N 4113 7.00 C 16039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.04 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG 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 j 1 " - " NAG j 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 163 " " NAG A2004 " - " ASN A 232 " " NAG A2005 " - " ASN A 601 " " NAG A2006 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 232 " " NAG B2003 " - " ASN B 329 " " NAG B2004 " - " ASN B 601 " " NAG B2005 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 329 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 280 " " NAG E 1 " - " ASN A 329 " " NAG F 1 " - " ASN A 341 " " NAG G 1 " - " ASN A 614 " " NAG H 1 " - " ASN A 707 " " NAG I 1 " - " ASN A 715 " " NAG J 1 " - " ASN A 799 " " NAG K 1 " - " ASN A1072 " " NAG L 1 " - " ASN A1096 " " NAG M 1 " - " ASN A1132 " " NAG N 1 " - " ASN B 122 " " NAG O 1 " - " ASN B 163 " " NAG P 1 " - " ASN B 280 " " NAG Q 1 " - " ASN B 341 " " NAG R 1 " - " ASN B 614 " " NAG S 1 " - " ASN B 707 " " NAG T 1 " - " ASN B 715 " " NAG U 1 " - " ASN B 799 " " NAG V 1 " - " ASN B1072 " " NAG W 1 " - " ASN B1096 " " NAG X 1 " - " ASN B1132 " " NAG Y 1 " - " ASN C 122 " " NAG Z 1 " - " ASN C 163 " " NAG a 1 " - " ASN C 232 " " NAG b 1 " - " ASN C 280 " " NAG c 1 " - " ASN C 341 " " NAG d 1 " - " ASN C 614 " " NAG e 1 " - " ASN C 707 " " NAG f 1 " - " ASN C 715 " " NAG g 1 " - " ASN C 799 " " NAG h 1 " - " ASN C1072 " " NAG i 1 " - " ASN C1096 " " NAG j 1 " - " ASN C1132 " Time building additional restraints: 10.28 Conformation dependent library (CDL) restraints added in 4.3 seconds 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5786 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 46 sheets defined 24.6% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.438A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 387 removed outlier: 4.277A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 735 through 742 Processing helix chain 'A' and resid 744 through 753 removed outlier: 4.097A pdb=" N GLN A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 781 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 882 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 939 removed outlier: 4.290A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS A 919 " --> pdb=" O TYR A 915 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.644A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.531A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.019A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 removed outlier: 3.582A pdb=" N LEU B 385 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.294A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.738A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.684A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.628A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 4.078A pdb=" N GLY B 889 " --> pdb=" O PHE B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.579A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 911 through 916' Processing helix chain 'B' and resid 917 through 939 Processing helix chain 'B' and resid 943 through 963 Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.552A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.351A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B1031 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.811A pdb=" N ASP B1144 " --> pdb=" O GLN B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 381 through 388 removed outlier: 4.549A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 408 removed outlier: 3.818A pdb=" N VAL C 405 " --> pdb=" O GLY C 402 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 408 " --> pdb=" O VAL C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.627A pdb=" N TYR C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 757 through 781 removed outlier: 3.511A pdb=" N LEU C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.597A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 910 through 939 removed outlier: 4.319A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS C 919 " --> pdb=" O TYR C 915 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU C 920 " --> pdb=" O GLU C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 removed outlier: 3.508A pdb=" N GLN C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 removed outlier: 3.715A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.434A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C1031 " --> pdb=" O MET C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1143 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.606A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.863A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.130A pdb=" N LEU A 84 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 103 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 126 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 128 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 130 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLU A 132 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASN A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLN A 134 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA A 161 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 317 removed outlier: 7.111A pdb=" N VAL A 593 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASN A 315 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY A 591 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 324 removed outlier: 3.790A pdb=" N ASN A 540 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA7, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AA8, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AA9, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.165A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.029A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 709 through 711 removed outlier: 3.511A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A1076 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE A1093 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.548A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.484A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB6, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB7, first strand: chain 'B' and resid 26 through 30 removed outlier: 8.615A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.164A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.506A pdb=" N LEU B 84 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.181A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.128A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.506A pdb=" N LEU B 84 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.345A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 326 removed outlier: 5.440A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 573 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 564 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC5, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.258A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AC7, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC8, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.007A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 699 through 701 removed outlier: 6.974A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.089A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.535A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1118 through 1120 Processing sheet with id=AD4, first strand: chain 'B' and resid 1092 through 1095 removed outlier: 5.081A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.620A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.517A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.075A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.195A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLU C 132 " --> pdb=" O CYS C 164 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N CYS C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N GLN C 134 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N ASN C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 309 through 317 removed outlier: 7.130A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 323 through 324 Processing sheet with id=AE1, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE2, first strand: chain 'C' and resid 359 through 360 removed outlier: 3.516A pdb=" N CYS C 523 " --> pdb=" O CYS C 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE4, first strand: chain 'C' and resid 471 through 472 removed outlier: 3.743A pdb=" N TYR C 471 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR C 487 " --> pdb=" O TYR C 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 564 through 565 removed outlier: 6.741A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.022A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 709 through 711 removed outlier: 3.570A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA C1076 " --> pdb=" O PHE C1093 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHE C1093 " --> pdb=" O ALA C1076 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLN C1104 " --> pdb=" O GLU C1109 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU C1109 " --> pdb=" O GLN C1104 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.540A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.516A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1118 through 1120 1006 hydrogen bonds defined for protein. 2748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.58 Time building geometry restraints manager: 11.13 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: 7977 1.34 - 1.46: 6421 1.46 - 1.58: 11272 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25802 Sorted by residual: bond pdb=" C PRO A 984 " pdb=" N PRO A 985 " ideal model delta sigma weight residual 1.333 1.376 -0.043 1.44e-02 4.82e+03 8.88e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" C1 NAG B2004 " pdb=" O5 NAG B2004 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.70e+00 ... (remaining 25797 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.95: 783 106.95 - 113.70: 14581 113.70 - 120.46: 9167 120.46 - 127.22: 10377 127.22 - 133.98: 201 Bond angle restraints: 35109 Sorted by residual: angle pdb=" C SER B 170 " pdb=" N GLN B 171 " pdb=" CA GLN B 171 " ideal model delta sigma weight residual 120.49 125.03 -4.54 1.42e+00 4.96e-01 1.02e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.55 -3.85 1.22e+00 6.72e-01 9.98e+00 angle pdb=" C ASN A 329 " pdb=" N ILE A 330 " pdb=" CA ILE A 330 " ideal model delta sigma weight residual 121.97 127.51 -5.54 1.80e+00 3.09e-01 9.47e+00 angle pdb=" N PRO A 559 " pdb=" CA PRO A 559 " pdb=" C PRO A 559 " ideal model delta sigma weight residual 112.47 118.68 -6.21 2.06e+00 2.36e-01 9.09e+00 angle pdb=" N PRO C 559 " pdb=" CA PRO C 559 " pdb=" C PRO C 559 " ideal model delta sigma weight residual 112.47 118.26 -5.79 2.06e+00 2.36e-01 7.89e+00 ... (remaining 35104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 14681 17.28 - 34.55: 1361 34.55 - 51.83: 299 51.83 - 69.10: 67 69.10 - 86.38: 34 Dihedral angle restraints: 16442 sinusoidal: 7455 harmonic: 8987 Sorted by residual: dihedral pdb=" CB CYS A 736 " pdb=" SG CYS A 736 " pdb=" SG CYS A 758 " pdb=" CB CYS A 758 " ideal model delta sinusoidal sigma weight residual -86.00 -0.91 -85.09 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS C 660 " pdb=" SG CYS C 660 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual -86.00 -169.13 83.13 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CB CYS A 289 " pdb=" SG CYS A 289 " pdb=" SG CYS A 299 " pdb=" CB CYS A 299 " ideal model delta sinusoidal sigma weight residual -86.00 -166.07 80.07 1 1.00e+01 1.00e-02 7.95e+01 ... (remaining 16439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3661 0.073 - 0.146: 539 0.146 - 0.219: 20 0.219 - 0.291: 1 0.291 - 0.364: 3 Chirality restraints: 4224 Sorted by residual: chirality pdb=" C1 NAG B2001 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B2001 " pdb=" O5 NAG B2001 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C1 NAG A2005 " pdb=" ND2 ASN A 601 " pdb=" C2 NAG A2005 " pdb=" O5 NAG A2005 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" C1 NAG A2004 " pdb=" ND2 ASN A 232 " pdb=" C2 NAG A2004 " pdb=" O5 NAG A2004 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 4221 not shown) Planarity restraints: 4490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " -0.025 2.00e-02 2.50e+03 2.31e-02 6.69e+00 pdb=" CG ASN A 329 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 558 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.06e+00 pdb=" N PRO C 559 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 559 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 559 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 983 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A 984 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.026 5.00e-02 4.00e+02 ... (remaining 4487 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1862 2.74 - 3.28: 24679 3.28 - 3.82: 39948 3.82 - 4.36: 44918 4.36 - 4.90: 80399 Nonbonded interactions: 191806 Sorted by model distance: nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.197 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.206 2.440 nonbonded pdb=" OG SER A 347 " pdb=" O ARG A 450 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR C 91 " pdb=" OE2 GLU C 189 " model vdw 2.226 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" OD2 ASP A 53 " model vdw 2.231 2.440 ... (remaining 191801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1144 or resid 2001 through 2004)) selection = (chain 'B' and (resid 14 through 619 or resid 635 through 825 or resid 853 throu \ gh 1144 or resid 2001 through 2004)) selection = (chain 'C' and (resid 14 through 619 or resid 635 through 1144 or resid 2001 thr \ ough 2004)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' 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' selection = chain 'j' } 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: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.310 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 67.030 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.440 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:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 : 0.004 0.049 25802 Z= 0.259 Angle : 0.590 7.739 35109 Z= 0.288 Chirality : 0.047 0.364 4224 Planarity : 0.004 0.050 4442 Dihedral : 13.700 86.376 10536 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.13 (0.15), residues: 3040 helix: 2.30 (0.22), residues: 656 sheet: 0.52 (0.19), residues: 719 loop : -1.07 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 434 HIS 0.002 0.000 HIS B1086 PHE 0.019 0.001 PHE B 904 TYR 0.016 0.001 TYR A 503 ARG 0.003 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 2.734 Fit side-chains revert: symmetry clash REVERT: A 569 ASP cc_start: 0.6995 (t0) cc_final: 0.6793 (OUTLIER) outliers start: 0 outliers final: 1 residues processed: 87 average time/residue: 1.1158 time to fit residues: 118.2822 Evaluate side-chains 61 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 259 optimal weight: 6.9990 chunk 232 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 179 optimal weight: 0.3980 chunk 278 optimal weight: 5.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25802 Z= 0.242 Angle : 0.542 9.272 35109 Z= 0.275 Chirality : 0.045 0.372 4224 Planarity : 0.004 0.049 4442 Dihedral : 7.453 58.443 5011 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 0.52 % Allowed : 6.52 % Favored : 92.97 % 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: 0.16 (0.15), residues: 3040 helix: 2.37 (0.22), residues: 664 sheet: 0.60 (0.19), residues: 709 loop : -1.12 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 434 HIS 0.003 0.001 HIS B1086 PHE 0.024 0.001 PHE A 166 TYR 0.016 0.001 TYR A1065 ARG 0.003 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 2.964 Fit side-chains revert: symmetry clash REVERT: A 569 ASP cc_start: 0.7010 (t0) cc_final: 0.6779 (OUTLIER) REVERT: A 898 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7919 (mtp) REVERT: A 988 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: B 867 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8102 (mtp) outliers start: 14 outliers final: 3 residues processed: 77 average time/residue: 1.1362 time to fit residues: 107.7309 Evaluate side-chains 66 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 898 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 154 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 232 optimal weight: 30.0000 chunk 189 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 301 optimal weight: 6.9990 chunk 248 optimal weight: 30.0000 chunk 276 optimal weight: 0.0770 chunk 95 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25802 Z= 0.207 Angle : 0.521 9.418 35109 Z= 0.264 Chirality : 0.045 0.360 4224 Planarity : 0.004 0.046 4442 Dihedral : 6.888 57.891 5011 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.76 % Rotamer: Outliers : 0.63 % Allowed : 9.48 % Favored : 89.89 % 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: 0.18 (0.15), residues: 3040 helix: 2.41 (0.21), residues: 662 sheet: 0.57 (0.19), residues: 717 loop : -1.10 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 434 HIS 0.002 0.001 HIS B1086 PHE 0.013 0.001 PHE C 904 TYR 0.016 0.001 TYR A1065 ARG 0.002 0.000 ARG B1037 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 3.241 Fit side-chains revert: symmetry clash REVERT: A 569 ASP cc_start: 0.6993 (t0) cc_final: 0.6747 (t0) REVERT: A 898 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7895 (mtp) REVERT: B 867 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8112 (mtp) outliers start: 17 outliers final: 8 residues processed: 75 average time/residue: 1.1172 time to fit residues: 103.5968 Evaluate side-chains 68 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 898 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 275 optimal weight: 0.0770 chunk 209 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 133 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 280 optimal weight: 3.9990 chunk 296 optimal weight: 0.0270 chunk 146 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25802 Z= 0.233 Angle : 0.524 9.477 35109 Z= 0.266 Chirality : 0.045 0.359 4224 Planarity : 0.004 0.046 4442 Dihedral : 6.542 57.517 5011 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.57 % Favored : 95.39 % Rotamer: Outliers : 1.11 % Allowed : 11.51 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3040 helix: 2.45 (0.21), residues: 657 sheet: 0.56 (0.19), residues: 712 loop : -1.08 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 351 HIS 0.003 0.001 HIS B1086 PHE 0.019 0.001 PHE A 106 TYR 0.016 0.001 TYR A1065 ARG 0.003 0.000 ARG B1037 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 63 time to evaluate : 3.068 Fit side-chains revert: symmetry clash REVERT: A 569 ASP cc_start: 0.7012 (t0) cc_final: 0.6756 (t0) REVERT: A 898 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7932 (mtp) REVERT: B 867 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8476 (mtp) outliers start: 30 outliers final: 11 residues processed: 85 average time/residue: 1.0551 time to fit residues: 111.8016 Evaluate side-chains 70 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain B residue 977 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 898 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 247 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 253 optimal weight: 0.7980 chunk 205 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 151 optimal weight: 7.9990 chunk 266 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN B 479 ASN C 269 GLN C 392 ASN ** C 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 25802 Z= 0.424 Angle : 0.619 11.532 35109 Z= 0.311 Chirality : 0.047 0.367 4224 Planarity : 0.004 0.047 4442 Dihedral : 6.593 57.747 5011 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.49 % Favored : 94.47 % Rotamer: Outliers : 1.37 % Allowed : 13.59 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3040 helix: 2.30 (0.21), residues: 655 sheet: 0.29 (0.18), residues: 743 loop : -1.15 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 884 HIS 0.003 0.001 HIS A1062 PHE 0.018 0.002 PHE B1119 TYR 0.017 0.001 TYR A1065 ARG 0.005 0.000 ARG B1037 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 58 time to evaluate : 3.014 Fit side-chains revert: symmetry clash REVERT: A 898 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.8023 (mtp) REVERT: B 466 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8955 (pp) REVERT: B 867 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8497 (mtp) outliers start: 37 outliers final: 15 residues processed: 86 average time/residue: 0.9579 time to fit residues: 104.2052 Evaluate side-chains 76 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 538 ASN Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 932 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 99 optimal weight: 0.9990 chunk 267 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 297 optimal weight: 3.9990 chunk 246 optimal weight: 0.3980 chunk 137 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25802 Z= 0.155 Angle : 0.524 11.709 35109 Z= 0.262 Chirality : 0.045 0.355 4224 Planarity : 0.004 0.047 4442 Dihedral : 6.160 59.091 5011 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 1.37 % Allowed : 14.55 % Favored : 84.08 % 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 (0.15), residues: 3040 helix: 2.48 (0.21), residues: 656 sheet: 0.60 (0.19), residues: 703 loop : -1.07 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 351 HIS 0.002 0.000 HIS B1086 PHE 0.017 0.001 PHE A 106 TYR 0.015 0.001 TYR B1065 ARG 0.001 0.000 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 62 time to evaluate : 2.891 Fit side-chains revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7252 (OUTLIER) cc_final: 0.6740 (p) REVERT: A 898 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7861 (mtp) REVERT: B 466 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8948 (pp) REVERT: B 867 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8295 (mtp) outliers start: 37 outliers final: 13 residues processed: 91 average time/residue: 0.9226 time to fit residues: 106.1872 Evaluate side-chains 76 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 538 ASN Chi-restraints excluded: chain C residue 643 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 286 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 chunk 165 optimal weight: 0.7980 chunk 295 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 180 optimal weight: 0.0670 chunk 136 optimal weight: 2.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25802 Z= 0.229 Angle : 0.534 12.166 35109 Z= 0.267 Chirality : 0.045 0.362 4224 Planarity : 0.004 0.047 4442 Dihedral : 6.043 57.425 5011 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.57 % Favored : 95.39 % Rotamer: Outliers : 1.52 % Allowed : 15.18 % Favored : 83.30 % 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 (0.15), residues: 3040 helix: 2.47 (0.21), residues: 657 sheet: 0.56 (0.19), residues: 711 loop : -1.04 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 884 HIS 0.003 0.001 HIS B1086 PHE 0.013 0.001 PHE C1119 TYR 0.016 0.001 TYR A1065 ARG 0.002 0.000 ARG B1037 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 58 time to evaluate : 3.127 Fit side-chains revert: symmetry clash REVERT: A 389 CYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7662 (p) REVERT: A 898 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7915 (mtp) REVERT: B 466 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8942 (pp) REVERT: B 867 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8367 (mtp) REVERT: B 1027 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8206 (tpp) outliers start: 41 outliers final: 21 residues processed: 90 average time/residue: 0.9383 time to fit residues: 107.4569 Evaluate side-chains 83 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 57 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1027 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 538 ASN Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 974 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 183 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 232 optimal weight: 20.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25802 Z= 0.264 Angle : 0.551 11.570 35109 Z= 0.278 Chirality : 0.045 0.361 4224 Planarity : 0.004 0.048 4442 Dihedral : 6.030 57.026 5011 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 1.37 % Allowed : 15.55 % Favored : 83.08 % 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: 0.18 (0.15), residues: 3040 helix: 2.45 (0.21), residues: 656 sheet: 0.53 (0.19), residues: 711 loop : -1.07 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 884 HIS 0.003 0.001 HIS B1086 PHE 0.022 0.001 PHE C 375 TYR 0.016 0.001 TYR A1065 ARG 0.003 0.000 ARG B1037 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 60 time to evaluate : 2.950 Fit side-chains revert: symmetry clash REVERT: A 898 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7940 (mtp) REVERT: B 466 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8916 (pp) REVERT: B 867 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8390 (mtp) REVERT: B 1027 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8240 (tpp) outliers start: 37 outliers final: 24 residues processed: 88 average time/residue: 0.9581 time to fit residues: 106.1180 Evaluate side-chains 85 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 57 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain B residue 1027 MET Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 538 ASN Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 736 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 269 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 chunk 258 optimal weight: 0.7980 chunk 275 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 216 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 249 optimal weight: 20.0000 chunk 260 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25802 Z= 0.178 Angle : 0.520 11.263 35109 Z= 0.260 Chirality : 0.044 0.358 4224 Planarity : 0.003 0.048 4442 Dihedral : 5.855 57.808 5011 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 1.22 % Allowed : 15.88 % Favored : 82.90 % 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 (0.15), residues: 3040 helix: 2.50 (0.21), residues: 659 sheet: 0.59 (0.19), residues: 710 loop : -1.01 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 884 HIS 0.002 0.000 HIS B1086 PHE 0.020 0.001 PHE C 375 TYR 0.018 0.001 TYR B 447 ARG 0.001 0.000 ARG B1105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 60 time to evaluate : 2.898 Fit side-chains revert: symmetry clash REVERT: A 898 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7892 (mtp) REVERT: B 867 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8335 (mtp) outliers start: 33 outliers final: 24 residues processed: 87 average time/residue: 0.9499 time to fit residues: 105.2662 Evaluate side-chains 82 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 56 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 538 ASN Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 736 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 181 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 281 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 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 237 GLN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25802 Z= 0.253 Angle : 0.550 13.720 35109 Z= 0.275 Chirality : 0.045 0.358 4224 Planarity : 0.004 0.049 4442 Dihedral : 5.911 56.960 5011 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.30 % Rotamer: Outliers : 1.15 % Allowed : 16.07 % Favored : 82.78 % 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: 0.24 (0.15), residues: 3040 helix: 2.59 (0.21), residues: 642 sheet: 0.54 (0.19), residues: 711 loop : -1.03 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 884 HIS 0.003 0.001 HIS B1086 PHE 0.021 0.001 PHE C 375 TYR 0.016 0.001 TYR A1065 ARG 0.003 0.000 ARG B1037 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 58 time to evaluate : 3.344 Fit side-chains revert: symmetry clash REVERT: A 898 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7932 (mtp) REVERT: B 867 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8387 (mtp) outliers start: 31 outliers final: 24 residues processed: 83 average time/residue: 0.9617 time to fit residues: 100.8756 Evaluate side-chains 81 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 55 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 538 ASN Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 736 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 193 optimal weight: 2.9990 chunk 259 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 243 optimal weight: 0.7980 chunk 102 optimal weight: 30.0000 chunk 250 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.086990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.051850 restraints weight = 85851.980| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 4.43 r_work: 0.2733 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25802 Z= 0.219 Angle : 0.540 12.930 35109 Z= 0.270 Chirality : 0.045 0.358 4224 Planarity : 0.004 0.048 4442 Dihedral : 5.868 57.242 5011 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 1.22 % Allowed : 16.18 % Favored : 82.60 % 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: 0.24 (0.15), residues: 3040 helix: 2.50 (0.21), residues: 649 sheet: 0.58 (0.19), residues: 709 loop : -1.02 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 351 HIS 0.003 0.001 HIS B1086 PHE 0.020 0.001 PHE C 375 TYR 0.017 0.001 TYR B 447 ARG 0.002 0.000 ARG B1037 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5192.65 seconds wall clock time: 95 minutes 33.40 seconds (5733.40 seconds total)