Starting phenix.real_space_refine on Mon Feb 19 19:14:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7k_20672/02_2024/6u7k_20672_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7k_20672/02_2024/6u7k_20672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7k_20672/02_2024/6u7k_20672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7k_20672/02_2024/6u7k_20672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7k_20672/02_2024/6u7k_20672_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7k_20672/02_2024/6u7k_20672_neut.pdb" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 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 16191 2.51 5 N 4029 2.21 5 O 5187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 365": "OE1" <-> "OE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 727": "OE1" <-> "OE2" Residue "A GLU 844": "OE1" <-> "OE2" Residue "A GLU 853": "OE1" <-> "OE2" Residue "A PHE 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 921": "NH1" <-> "NH2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A GLU 1012": "OE1" <-> "OE2" Residue "A GLU 1016": "OE1" <-> "OE2" Residue "A GLU 1104": "OE1" <-> "OE2" Residue "A ARG 1126": "NH1" <-> "NH2" Residue "A GLU 1174": "OE1" <-> "OE2" Residue "A GLU 1190": "OE1" <-> "OE2" Residue "A GLU 1198": "OE1" <-> "OE2" Residue "A PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1221": "OE1" <-> "OE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 623": "OE1" <-> "OE2" Residue "B TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 727": "OE1" <-> "OE2" Residue "B GLU 853": "OE1" <-> "OE2" Residue "B ARG 921": "NH1" <-> "NH2" Residue "B ASP 925": "OD1" <-> "OD2" Residue "B GLU 945": "OE1" <-> "OE2" Residue "B GLU 1012": "OE1" <-> "OE2" Residue "B GLU 1016": "OE1" <-> "OE2" Residue "B ARG 1126": "NH1" <-> "NH2" Residue "B GLU 1174": "OE1" <-> "OE2" Residue "B GLU 1190": "OE1" <-> "OE2" Residue "B GLU 1198": "OE1" <-> "OE2" Residue "B GLU 1221": "OE1" <-> "OE2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 544": "NH1" <-> "NH2" Residue "C PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 623": "OE1" <-> "OE2" Residue "C TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 727": "OE1" <-> "OE2" Residue "C GLU 853": "OE1" <-> "OE2" Residue "C GLU 854": "OE1" <-> "OE2" Residue "C ARG 921": "NH1" <-> "NH2" Residue "C GLU 945": "OE1" <-> "OE2" Residue "C GLU 1012": "OE1" <-> "OE2" Residue "C GLU 1016": "OE1" <-> "OE2" Residue "C ARG 1126": "NH1" <-> "NH2" Residue "C GLU 1174": "OE1" <-> "OE2" Residue "C GLU 1190": "OE1" <-> "OE2" Residue "C GLU 1198": "OE1" <-> "OE2" Residue "C GLU 1221": "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: 25515 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8139 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 36, 'TRANS': 1027} Chain breaks: 6 Chain: "B" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8139 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 36, 'TRANS': 1027} Chain breaks: 6 Chain: "C" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8139 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 36, 'TRANS': 1027} Chain breaks: 6 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} 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: "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: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 13.58, per 1000 atoms: 0.53 Number of scatterers: 25515 At special positions: 0 Unit cell: (147.275, 155.875, 159.1, 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 5187 8.00 N 4029 7.00 C 16191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 304 " distance=2.06 Simple disulfide: pdb=" SG CYS A 346 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 470 " distance=2.01 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 586 " distance=2.04 Simple disulfide: pdb=" SG CYS A 569 " - pdb=" SG CYS A 596 " distance=2.01 Simple disulfide: pdb=" SG CYS A 646 " - pdb=" SG CYS A 697 " distance=2.04 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 754 " distance=2.04 Simple disulfide: pdb=" SG CYS A 805 " - pdb=" SG CYS A 827 " distance=2.04 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS A 816 " distance=2.04 Simple disulfide: pdb=" SG CYS A 917 " - pdb=" SG CYS A 928 " distance=2.05 Simple disulfide: pdb=" SG CYS A1119 " - pdb=" SG CYS A1130 " distance=1.99 Simple disulfide: pdb=" SG CYS A1170 " - pdb=" SG CYS A1223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 227 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 304 " distance=2.01 Simple disulfide: pdb=" SG CYS B 346 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 461 " - pdb=" SG CYS B 470 " distance=2.00 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 586 " distance=2.04 Simple disulfide: pdb=" SG CYS B 569 " - pdb=" SG CYS B 596 " distance=2.00 Simple disulfide: pdb=" SG CYS B 646 " - pdb=" SG CYS B 697 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 754 " distance=2.00 Simple disulfide: pdb=" SG CYS B 805 " - pdb=" SG CYS B 827 " distance=2.04 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 816 " distance=2.10 Simple disulfide: pdb=" SG CYS B 917 " - pdb=" SG CYS B 928 " distance=2.05 Simple disulfide: pdb=" SG CYS B1119 " - pdb=" SG CYS B1130 " distance=1.99 Simple disulfide: pdb=" SG CYS B1170 " - pdb=" SG CYS B1223 " distance=2.04 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 304 " distance=2.02 Simple disulfide: pdb=" SG CYS C 346 " - pdb=" SG CYS C 370 " distance=2.05 Simple disulfide: pdb=" SG CYS C 461 " - pdb=" SG CYS C 470 " distance=2.00 Simple disulfide: pdb=" SG CYS C 540 " - pdb=" SG CYS C 586 " distance=2.04 Simple disulfide: pdb=" SG CYS C 569 " - pdb=" SG CYS C 596 " distance=2.03 Simple disulfide: pdb=" SG CYS C 646 " - pdb=" SG CYS C 697 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 754 " distance=2.03 Simple disulfide: pdb=" SG CYS C 805 " - pdb=" SG CYS C 827 " distance=2.03 Simple disulfide: pdb=" SG CYS C 810 " - pdb=" SG CYS C 816 " distance=2.04 Simple disulfide: pdb=" SG CYS C 917 " - pdb=" SG CYS C 928 " distance=2.01 Simple disulfide: pdb=" SG CYS C1119 " - pdb=" SG CYS C1130 " distance=2.00 Simple disulfide: pdb=" SG CYS C1170 " - pdb=" SG CYS C1223 " distance=2.05 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 Atom "HETATM24769 O5 NAG M 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM24953 O5 NAG R 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM24925 O5 NAG Q 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN I 4 " - " MAN I 5 " " MAN N 4 " - " MAN N 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA I 3 " - " MAN I 4 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA I 3 " - " MAN I 6 " " BMA N 3 " - " MAN N 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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 I 2 " - " BMA I 3 " " 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 N 2 " - " BMA N 3 " " 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-ASN " NAG A1401 " - " ASN A 213 " " NAG A1408 " - " ASN A 297 " " NAG A1411 " - " ASN A 341 " " NAG A1412 " - " ASN A 348 " " NAG A1413 " - " ASN A 422 " " NAG A1416 " - " ASN A 553 " " NAG A1417 " - " ASN A 664 " " NAG A1420 " - " ASN A 723 " " NAG A1421 " - " ASN A 740 " " NAG A1422 " - " ASN A 778 " " NAG A1423 " - " ASN A 784 " " NAG A1426 " - " ASN A1006 " " NAG A1427 " - " ASN A1229 " " NAG B1401 " - " ASN B 213 " " NAG B1408 " - " ASN B 297 " " NAG B1411 " - " ASN B 341 " " NAG B1412 " - " ASN B 348 " " NAG B1413 " - " ASN B 422 " " NAG B1416 " - " ASN B 553 " " NAG B1417 " - " ASN B 664 " " NAG B1420 " - " ASN B 723 " " NAG B1421 " - " ASN B 740 " " NAG B1422 " - " ASN B 778 " " NAG B1423 " - " ASN B 784 " " NAG B1426 " - " ASN B1006 " " NAG B1427 " - " ASN B1229 " " NAG C1401 " - " ASN C 213 " " NAG C1408 " - " ASN C 297 " " NAG C1411 " - " ASN C 341 " " NAG C1412 " - " ASN C 348 " " NAG C1413 " - " ASN C 422 " " NAG C1416 " - " ASN C 553 " " NAG C1417 " - " ASN C 664 " " NAG C1420 " - " ASN C 723 " " NAG C1421 " - " ASN C 740 " " NAG C1422 " - " ASN C 778 " " NAG C1423 " - " ASN C 784 " " NAG C1426 " - " ASN C1006 " " NAG C1427 " - " ASN C1229 " " NAG D 1 " - " ASN A 261 " " NAG E 1 " - " ASN A 321 " " NAG F 1 " - " ASN A 511 " " NAG G 1 " - " ASN A 685 " " NAG H 1 " - " ASN A 870 " " NAG I 1 " - " ASN B 261 " " NAG J 1 " - " ASN B 321 " " NAG K 1 " - " ASN B 511 " " NAG L 1 " - " ASN B 685 " " NAG M 1 " - " ASN B 870 " " NAG N 1 " - " ASN C 261 " " NAG O 1 " - " ASN C 321 " " NAG P 1 " - " ASN C 511 " " NAG Q 1 " - " ASN C 685 " " NAG R 1 " - " ASN C 870 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.90 Conformation dependent library (CDL) restraints added in 4.9 seconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5934 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 43 sheets defined 23.8% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 246 removed outlier: 4.239A pdb=" N HIS A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 463 through 470 Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.694A pdb=" N ASN A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 811 Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 827 through 849 removed outlier: 4.673A pdb=" N ALA A 833 " --> pdb=" O THR A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 860 removed outlier: 4.696A pdb=" N LEU A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 876 removed outlier: 4.220A pdb=" N GLY A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 903 removed outlier: 3.640A pdb=" N VAL A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 933 removed outlier: 3.675A pdb=" N TYR A 931 " --> pdb=" O VAL A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 957 Processing helix chain 'A' and resid 970 through 981 removed outlier: 3.678A pdb=" N ALA A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 981 " --> pdb=" O ALA A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1011 removed outlier: 3.905A pdb=" N SER A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER A1009 " --> pdb=" O GLY A1005 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A1010 " --> pdb=" O ASN A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1018 Processing helix chain 'A' and resid 1019 through 1024 removed outlier: 3.647A pdb=" N GLY A1024 " --> pdb=" O THR A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1040 Processing helix chain 'A' and resid 1043 through 1052 removed outlier: 3.775A pdb=" N GLN A1052 " --> pdb=" O GLN A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1055 No H-bonds generated for 'chain 'A' and resid 1053 through 1055' Processing helix chain 'A' and resid 1063 through 1068 Processing helix chain 'A' and resid 1072 through 1120 removed outlier: 4.293A pdb=" N VAL A1078 " --> pdb=" O LEU A1074 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A1082 " --> pdb=" O VAL A1078 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A1083 " --> pdb=" O GLN A1079 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A1107 " --> pdb=" O THR A1103 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER A1108 " --> pdb=" O GLU A1104 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A1111 " --> pdb=" O ALA A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1239 removed outlier: 3.823A pdb=" N VAL A1238 " --> pdb=" O GLN A1234 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 3.692A pdb=" N ALA B 235 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 removed outlier: 4.240A pdb=" N HIS B 246 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 326 removed outlier: 3.509A pdb=" N ILE B 326 " --> pdb=" O THR B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 473 removed outlier: 3.681A pdb=" N LEU B 468 " --> pdb=" O PRO B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 577 removed outlier: 3.654A pdb=" N ASN B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 811 Processing helix chain 'B' and resid 813 through 821 removed outlier: 3.723A pdb=" N GLN B 818 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 819 " --> pdb=" O ARG B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 847 removed outlier: 4.632A pdb=" N ALA B 833 " --> pdb=" O THR B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 860 removed outlier: 3.509A pdb=" N GLN B 857 " --> pdb=" O GLU B 853 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU B 858 " --> pdb=" O GLU B 854 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B 859 " --> pdb=" O ALA B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 876 removed outlier: 4.258A pdb=" N GLY B 876 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 904 removed outlier: 3.990A pdb=" N VAL B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 919 removed outlier: 3.984A pdb=" N SER B 918 " --> pdb=" O TYR B 914 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN B 919 " --> pdb=" O LYS B 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 914 through 919' Processing helix chain 'B' and resid 925 through 933 removed outlier: 3.837A pdb=" N TYR B 931 " --> pdb=" O VAL B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 957 Processing helix chain 'B' and resid 970 through 981 removed outlier: 3.510A pdb=" N ALA B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B 981 " --> pdb=" O ALA B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1009 removed outlier: 3.860A pdb=" N SER B1002 " --> pdb=" O GLU B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1018 Processing helix chain 'B' and resid 1019 through 1024 removed outlier: 3.585A pdb=" N GLY B1024 " --> pdb=" O THR B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1041 Processing helix chain 'B' and resid 1043 through 1052 removed outlier: 3.587A pdb=" N LEU B1049 " --> pdb=" O ALA B1045 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B1052 " --> pdb=" O GLN B1048 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1070 Processing helix chain 'B' and resid 1072 through 1120 removed outlier: 3.850A pdb=" N ASP B1077 " --> pdb=" O ILE B1073 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B1078 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B1082 " --> pdb=" O VAL B1078 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B1107 " --> pdb=" O THR B1103 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B1108 " --> pdb=" O GLU B1104 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B1111 " --> pdb=" O ALA B1107 " (cutoff:3.500A) Processing helix chain 'B' and resid 1234 through 1239 removed outlier: 3.825A pdb=" N VAL B1238 " --> pdb=" O GLN B1234 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 326 Processing helix chain 'C' and resid 463 through 472 removed outlier: 3.822A pdb=" N LEU C 468 " --> pdb=" O PRO C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 577 removed outlier: 3.679A pdb=" N ASN C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 811 Processing helix chain 'C' and resid 813 through 821 Processing helix chain 'C' and resid 825 through 849 removed outlier: 4.351A pdb=" N ALA C 833 " --> pdb=" O THR C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 860 removed outlier: 4.912A pdb=" N LEU C 858 " --> pdb=" O GLU C 854 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C 859 " --> pdb=" O ALA C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 876 removed outlier: 4.421A pdb=" N GLY C 876 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 901 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.903A pdb=" N ARG C 916 " --> pdb=" O ASP C 913 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER C 918 " --> pdb=" O LYS C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 933 removed outlier: 4.132A pdb=" N TYR C 931 " --> pdb=" O VAL C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 956 Processing helix chain 'C' and resid 957 through 960 Processing helix chain 'C' and resid 970 through 981 removed outlier: 3.609A pdb=" N ALA C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1009 Processing helix chain 'C' and resid 1014 through 1018 Processing helix chain 'C' and resid 1019 through 1024 removed outlier: 3.703A pdb=" N GLY C1024 " --> pdb=" O THR C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1042 Processing helix chain 'C' and resid 1043 through 1052 removed outlier: 3.575A pdb=" N GLN C1052 " --> pdb=" O GLN C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1063 through 1069 Processing helix chain 'C' and resid 1072 through 1119 removed outlier: 3.524A pdb=" N ASP C1077 " --> pdb=" O ILE C1073 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C1078 " --> pdb=" O LEU C1074 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG C1082 " --> pdb=" O VAL C1078 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C1107 " --> pdb=" O THR C1103 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER C1108 " --> pdb=" O GLU C1104 " (cutoff:3.500A) Processing helix chain 'C' and resid 1234 through 1239 removed outlier: 3.529A pdb=" N VAL C1238 " --> pdb=" O GLN C1234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51 removed outlier: 4.262A pdb=" N TYR A 209 " --> pdb=" O CYS A 227 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR A 223 " --> pdb=" O ASN A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 181 removed outlier: 3.504A pdb=" N GLY A 75 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 285 removed outlier: 3.544A pdb=" N LEU A 276 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN A 442 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 278 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER A 440 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS A 280 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 438 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 282 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP A 436 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 437 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 403 " --> pdb=" O TYR A 410 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 285 removed outlier: 3.544A pdb=" N LEU A 276 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN A 442 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 278 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER A 440 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS A 280 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 438 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 282 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP A 436 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASP A 445 " --> pdb=" O TYR A 460 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TYR A 460 " --> pdb=" O ASP A 445 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 447 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 458 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU A 449 " --> pdb=" O GLN A 456 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 295 removed outlier: 3.548A pdb=" N GLN A 292 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 418 " --> pdb=" O HIS A 335 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE A 332 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 368 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A 387 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N CYS A 370 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 480 through 485 removed outlier: 3.691A pdb=" N GLY A 712 " --> pdb=" O ALA A 704 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 706 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE A 710 " --> pdb=" O VAL A 706 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 496 through 499 removed outlier: 4.301A pdb=" N VAL A 691 " --> pdb=" O THR A 663 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU A 681 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 525 through 533 removed outlier: 4.428A pdb=" N SER A 529 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 515 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR A 531 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR A 513 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE A 533 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN A 511 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 547 " --> pdb=" O SER A 508 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 516 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR A 616 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL A 587 " --> pdb=" O TYR A 616 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN A 618 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE A 585 " --> pdb=" O GLN A 618 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR A 620 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 622 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER A 581 " --> pdb=" O GLY A 622 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 525 through 533 removed outlier: 4.428A pdb=" N SER A 529 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 515 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR A 531 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR A 513 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE A 533 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN A 511 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 547 " --> pdb=" O SER A 508 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 516 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LYS A 611 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLY A 602 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 562 " --> pdb=" O TYR A 603 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 744 through 748 Processing sheet with id=AB2, first strand: chain 'A' and resid 778 through 782 Processing sheet with id=AB3, first strand: chain 'A' and resid 785 through 795 removed outlier: 7.071A pdb=" N GLY A1147 " --> pdb=" O ALA A1143 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA A1143 " --> pdb=" O GLY A1147 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A1149 " --> pdb=" O VAL A1141 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A1141 " --> pdb=" O LEU A1149 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU A1151 " --> pdb=" O SER A1139 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER A1139 " --> pdb=" O LEU A1151 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A1153 " --> pdb=" O ILE A1137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 801 through 803 Processing sheet with id=AB5, first strand: chain 'A' and resid 1217 through 1220 removed outlier: 4.547A pdb=" N ALA A1176 " --> pdb=" O ILE A1220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 46 through 49 removed outlier: 4.191A pdb=" N TYR B 209 " --> pdb=" O CYS B 227 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 177 through 181 removed outlier: 3.528A pdb=" N GLY B 162 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 268 through 285 removed outlier: 3.689A pdb=" N LEU B 276 " --> pdb=" O ASN B 442 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN B 442 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL B 278 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER B 440 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS B 280 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 438 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 282 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP B 436 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 403 " --> pdb=" O TYR B 410 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 268 through 285 removed outlier: 3.689A pdb=" N LEU B 276 " --> pdb=" O ASN B 442 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN B 442 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL B 278 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER B 440 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS B 280 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 438 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 282 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP B 436 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASP B 445 " --> pdb=" O TYR B 460 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR B 460 " --> pdb=" O ASP B 445 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU B 447 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE B 458 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU B 449 " --> pdb=" O GLN B 456 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 290 through 295 removed outlier: 6.949A pdb=" N HIS B 335 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL B 419 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 333 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE B 332 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR B 368 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL B 387 " --> pdb=" O TYR B 368 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N CYS B 370 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 480 through 485 removed outlier: 3.867A pdb=" N GLY B 712 " --> pdb=" O ALA B 704 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 706 " --> pdb=" O ILE B 710 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 496 through 499 removed outlier: 4.286A pdb=" N VAL B 691 " --> pdb=" O THR B 663 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU B 681 " --> pdb=" O VAL B 694 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 525 through 533 removed outlier: 4.447A pdb=" N SER B 529 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER B 515 " --> pdb=" O SER B 529 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 531 " --> pdb=" O THR B 513 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B 513 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE B 533 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN B 511 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 547 " --> pdb=" O SER B 508 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS B 584 " --> pdb=" O THR B 620 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLY B 622 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE B 582 " --> pdb=" O GLY B 622 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 525 through 533 removed outlier: 4.447A pdb=" N SER B 529 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER B 515 " --> pdb=" O SER B 529 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 531 " --> pdb=" O THR B 513 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B 513 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE B 533 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN B 511 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 547 " --> pdb=" O SER B 508 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LYS B 611 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLY B 602 " --> pdb=" O LYS B 611 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER B 562 " --> pdb=" O TYR B 603 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 746 through 748 Processing sheet with id=AC7, first strand: chain 'B' and resid 778 through 782 removed outlier: 4.589A pdb=" N LEU B1186 " --> pdb=" O ILE B1166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 785 through 795 removed outlier: 3.815A pdb=" N PHE B1138 " --> pdb=" O THR B1153 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU B1155 " --> pdb=" O HIS B1136 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS B1136 " --> pdb=" O LEU B1155 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 801 through 803 Processing sheet with id=AD1, first strand: chain 'B' and resid 1217 through 1220 removed outlier: 4.416A pdb=" N ALA B1176 " --> pdb=" O ILE B1220 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B1230 " --> pdb=" O CYS B1170 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.433A pdb=" N TYR C 223 " --> pdb=" O ASN C 213 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 177 through 181 Processing sheet with id=AD4, first strand: chain 'C' and resid 268 through 285 removed outlier: 5.538A pdb=" N LYS C 269 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 450 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL C 271 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 448 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASN C 273 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA C 446 " --> pdb=" O ASN C 273 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 444 " --> pdb=" O PRO C 275 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER C 440 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 281 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE C 438 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA C 283 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP C 436 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL C 403 " --> pdb=" O TYR C 410 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 268 through 285 removed outlier: 5.538A pdb=" N LYS C 269 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 450 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL C 271 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 448 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASN C 273 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA C 446 " --> pdb=" O ASN C 273 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 444 " --> pdb=" O PRO C 275 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER C 440 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 281 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE C 438 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA C 283 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP C 436 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASP C 445 " --> pdb=" O TYR C 460 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TYR C 460 " --> pdb=" O ASP C 445 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 447 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE C 458 " --> pdb=" O LEU C 447 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU C 449 " --> pdb=" O GLN C 456 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 290 through 295 removed outlier: 3.605A pdb=" N GLN C 292 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N HIS C 335 " --> pdb=" O ASP C 417 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL C 419 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C 333 " --> pdb=" O VAL C 419 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE C 332 " --> pdb=" O PHE C 344 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR C 368 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL C 387 " --> pdb=" O TYR C 368 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS C 370 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 480 through 485 removed outlier: 3.647A pdb=" N GLY C 712 " --> pdb=" O ALA C 704 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 706 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE C 710 " --> pdb=" O VAL C 706 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 496 through 499 removed outlier: 3.511A pdb=" N GLY C 656 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL C 691 " --> pdb=" O THR C 663 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU C 681 " --> pdb=" O VAL C 694 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR C 673 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 525 through 533 removed outlier: 5.440A pdb=" N LEU C 526 " --> pdb=" O GLY C 519 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY C 519 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA C 528 " --> pdb=" O ALA C 517 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA C 517 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 510 " --> pdb=" O THR C 549 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N PHE C 551 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE C 512 " --> pdb=" O PHE C 551 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 538 through 540 removed outlier: 5.288A pdb=" N SER C 581 " --> pdb=" O GLY C 622 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY C 622 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR C 620 " --> pdb=" O SER C 583 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE C 585 " --> pdb=" O GLN C 618 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLN C 618 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL C 587 " --> pdb=" O TYR C 616 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR C 616 " --> pdb=" O VAL C 587 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 538 through 540 removed outlier: 5.288A pdb=" N SER C 581 " --> pdb=" O GLY C 622 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY C 622 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR C 620 " --> pdb=" O SER C 583 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE C 585 " --> pdb=" O GLN C 618 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLN C 618 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL C 587 " --> pdb=" O TYR C 616 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR C 616 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS C 611 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY C 602 " --> pdb=" O LYS C 611 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER C 562 " --> pdb=" O TYR C 603 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 744 through 748 Processing sheet with id=AE4, first strand: chain 'C' and resid 778 through 782 Processing sheet with id=AE5, first strand: chain 'C' and resid 785 through 795 removed outlier: 7.010A pdb=" N GLY C1147 " --> pdb=" O ALA C1143 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA C1143 " --> pdb=" O GLY C1147 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C1149 " --> pdb=" O VAL C1141 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL C1141 " --> pdb=" O LEU C1149 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU C1151 " --> pdb=" O SER C1139 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER C1139 " --> pdb=" O LEU C1151 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR C1153 " --> pdb=" O ILE C1137 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 801 through 803 Processing sheet with id=AE7, first strand: chain 'C' and resid 1217 through 1220 removed outlier: 4.425A pdb=" N ALA C1176 " --> pdb=" O ILE C1220 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2697 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: 13.04 Time building geometry restraints manager: 11.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 183 1.21 - 1.36: 8094 1.36 - 1.51: 8447 1.51 - 1.67: 9151 1.67 - 1.82: 138 Bond restraints: 26013 Sorted by residual: bond pdb=" C ASN A 511 " pdb=" O ASN A 511 " ideal model delta sigma weight residual 1.236 1.056 0.180 1.24e-02 6.50e+03 2.11e+02 bond pdb=" C ASN C 422 " pdb=" O ASN C 422 " ideal model delta sigma weight residual 1.232 1.081 0.151 1.12e-02 7.97e+03 1.81e+02 bond pdb=" C ASN A 422 " pdb=" O ASN A 422 " ideal model delta sigma weight residual 1.232 1.103 0.128 1.01e-02 9.80e+03 1.61e+02 bond pdb=" CA ASN B 422 " pdb=" CB ASN B 422 " ideal model delta sigma weight residual 1.527 1.432 0.096 7.60e-03 1.73e+04 1.58e+02 bond pdb=" C ASN C 511 " pdb=" O ASN C 511 " ideal model delta sigma weight residual 1.235 1.102 0.132 1.18e-02 7.18e+03 1.26e+02 ... (remaining 26008 not shown) Histogram of bond angle deviations from ideal: 80.67 - 92.04: 13 92.04 - 103.41: 389 103.41 - 114.78: 15083 114.78 - 126.15: 19389 126.15 - 137.52: 571 Bond angle restraints: 35445 Sorted by residual: angle pdb=" N ASN B 723 " pdb=" CA ASN B 723 " pdb=" C ASN B 723 " ideal model delta sigma weight residual 113.20 127.33 -14.13 1.21e+00 6.83e-01 1.36e+02 angle pdb=" N ASN C 723 " pdb=" CA ASN C 723 " pdb=" C ASN C 723 " ideal model delta sigma weight residual 113.18 126.88 -13.70 1.21e+00 6.83e-01 1.28e+02 angle pdb=" N ASN A 723 " pdb=" CA ASN A 723 " pdb=" C ASN A 723 " ideal model delta sigma weight residual 113.02 125.75 -12.73 1.20e+00 6.94e-01 1.13e+02 angle pdb=" N ASN B 348 " pdb=" CA ASN B 348 " pdb=" CB ASN B 348 " ideal model delta sigma weight residual 110.32 92.41 17.91 1.70e+00 3.46e-01 1.11e+02 angle pdb=" N ASN C 685 " pdb=" CA ASN C 685 " pdb=" C ASN C 685 " ideal model delta sigma weight residual 108.20 91.78 16.42 1.71e+00 3.42e-01 9.22e+01 ... (remaining 35440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.12: 15562 24.12 - 48.24: 666 48.24 - 72.35: 113 72.35 - 96.47: 44 96.47 - 120.59: 10 Dihedral angle restraints: 16395 sinusoidal: 7128 harmonic: 9267 Sorted by residual: dihedral pdb=" N ASN B 348 " pdb=" C ASN B 348 " pdb=" CA ASN B 348 " pdb=" CB ASN B 348 " ideal model delta harmonic sigma weight residual 122.80 99.57 23.23 0 2.50e+00 1.60e-01 8.64e+01 dihedral pdb=" N ASN A 213 " pdb=" C ASN A 213 " pdb=" CA ASN A 213 " pdb=" CB ASN A 213 " ideal model delta harmonic sigma weight residual 122.80 145.66 -22.86 0 2.50e+00 1.60e-01 8.36e+01 dihedral pdb=" C ASN A 213 " pdb=" N ASN A 213 " pdb=" CA ASN A 213 " pdb=" CB ASN A 213 " ideal model delta harmonic sigma weight residual -122.60 -145.02 22.42 0 2.50e+00 1.60e-01 8.04e+01 ... (remaining 16392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.868: 4364 0.868 - 1.736: 24 1.736 - 2.605: 14 2.605 - 3.473: 11 3.473 - 4.341: 3 Chirality restraints: 4416 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 0.80 -3.20 2.00e-02 2.50e+03 2.55e+04 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 0.35 -2.75 2.00e-02 2.50e+03 1.90e+04 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.12 -2.28 2.00e-02 2.50e+03 1.30e+04 ... (remaining 4413 not shown) Planarity restraints: 4473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1412 " -0.414 2.00e-02 2.50e+03 3.35e-01 1.40e+03 pdb=" C7 NAG A1412 " 0.119 2.00e-02 2.50e+03 pdb=" C8 NAG A1412 " -0.223 2.00e-02 2.50e+03 pdb=" N2 NAG A1412 " 0.568 2.00e-02 2.50e+03 pdb=" O7 NAG A1412 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1427 " 0.398 2.00e-02 2.50e+03 3.19e-01 1.28e+03 pdb=" C7 NAG B1427 " -0.117 2.00e-02 2.50e+03 pdb=" C8 NAG B1427 " 0.231 2.00e-02 2.50e+03 pdb=" N2 NAG B1427 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG B1427 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1401 " 0.368 2.00e-02 2.50e+03 3.15e-01 1.24e+03 pdb=" C7 NAG B1401 " -0.090 2.00e-02 2.50e+03 pdb=" C8 NAG B1401 " 0.052 2.00e-02 2.50e+03 pdb=" N2 NAG B1401 " -0.549 2.00e-02 2.50e+03 pdb=" O7 NAG B1401 " 0.219 2.00e-02 2.50e+03 ... (remaining 4470 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 12 2.05 - 2.76: 2045 2.76 - 3.48: 34642 3.48 - 4.19: 58657 4.19 - 4.90: 103744 Nonbonded interactions: 199100 Sorted by model distance: nonbonded pdb=" OD2 ASP B 431 " pdb=" O6 NAG J 1 " model vdw 1.341 2.440 nonbonded pdb=" OD2 ASP B 431 " pdb=" C6 NAG J 1 " model vdw 1.602 3.440 nonbonded pdb=" OD2 ASP A 431 " pdb=" O6 NAG E 1 " model vdw 1.603 2.440 nonbonded pdb=" OD2 ASP A 431 " pdb=" C6 NAG E 1 " model vdw 1.743 3.440 nonbonded pdb=" OG SER C1139 " pdb=" ND1 HIS C1152 " model vdw 1.826 2.520 ... (remaining 199095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 17.660 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 73.110 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 : 0.017 0.180 26013 Z= 1.122 Angle : 2.301 28.058 35445 Z= 1.386 Chirality : 0.273 4.341 4416 Planarity : 0.028 0.335 4419 Dihedral : 14.729 120.591 10344 Min Nonbonded Distance : 1.341 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.66 % Allowed : 5.65 % Favored : 91.68 % Cbeta Deviations : 2.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 3150 helix: -2.24 (0.16), residues: 615 sheet: 0.71 (0.20), residues: 618 loop : -1.01 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.112 0.023 TRP B 165 HIS 0.011 0.004 HIS A 507 PHE 0.074 0.015 PHE B 408 TYR 0.162 0.025 TYR C 950 ARG 0.013 0.002 ARG C1210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 489 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 HIS cc_start: 0.7496 (m-70) cc_final: 0.7010 (m-70) REVERT: A 290 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8326 (pt) REVERT: A 322 ASP cc_start: 0.7563 (t0) cc_final: 0.7266 (t0) REVERT: A 583 SER cc_start: 0.8680 (t) cc_final: 0.8257 (p) REVERT: A 679 GLN cc_start: 0.7546 (tt0) cc_final: 0.7182 (tp40) REVERT: A 737 ASP cc_start: 0.7684 (t0) cc_final: 0.7396 (t0) REVERT: A 745 VAL cc_start: 0.8814 (m) cc_final: 0.8586 (t) REVERT: A 867 ASP cc_start: 0.7338 (t70) cc_final: 0.6786 (t0) REVERT: A 933 SER cc_start: 0.8642 (m) cc_final: 0.8177 (p) REVERT: A 935 VAL cc_start: 0.9000 (p) cc_final: 0.8542 (m) REVERT: A 994 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7140 (mm110) REVERT: A 1068 TYR cc_start: 0.8403 (m-80) cc_final: 0.7989 (m-80) REVERT: A 1135 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6776 (mm-30) REVERT: A 1175 ILE cc_start: 0.8031 (pt) cc_final: 0.6700 (pt) REVERT: B 209 TYR cc_start: 0.7811 (m-80) cc_final: 0.7534 (m-10) REVERT: B 234 TYR cc_start: 0.7574 (t80) cc_final: 0.7246 (t80) REVERT: B 450 VAL cc_start: 0.8433 (t) cc_final: 0.8200 (m) REVERT: B 566 ASP cc_start: 0.7464 (t0) cc_final: 0.7209 (t0) REVERT: B 578 ASP cc_start: 0.7790 (t0) cc_final: 0.7340 (t70) REVERT: B 583 SER cc_start: 0.8626 (t) cc_final: 0.8308 (p) REVERT: B 588 SER cc_start: 0.8505 (t) cc_final: 0.8130 (t) REVERT: B 599 ASP cc_start: 0.7441 (m-30) cc_final: 0.7223 (m-30) REVERT: B 635 ILE cc_start: 0.8855 (mm) cc_final: 0.8651 (mt) REVERT: B 641 MET cc_start: 0.8200 (mtm) cc_final: 0.7964 (mtt) REVERT: B 809 VAL cc_start: 0.8504 (t) cc_final: 0.8168 (m) REVERT: B 815 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8106 (tpp-160) REVERT: B 851 ILE cc_start: 0.8459 (mp) cc_final: 0.8234 (mm) REVERT: B 867 ASP cc_start: 0.7695 (t0) cc_final: 0.7212 (t0) REVERT: B 913 ASP cc_start: 0.7904 (p0) cc_final: 0.7589 (p0) REVERT: B 933 SER cc_start: 0.8617 (m) cc_final: 0.8262 (p) REVERT: B 994 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7166 (tp40) REVERT: B 1135 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6781 (mm-30) REVERT: C 450 VAL cc_start: 0.8232 (t) cc_final: 0.8008 (m) REVERT: C 568 ASN cc_start: 0.7641 (t160) cc_final: 0.7410 (t0) REVERT: C 578 ASP cc_start: 0.7446 (t70) cc_final: 0.6998 (t0) REVERT: C 583 SER cc_start: 0.8809 (t) cc_final: 0.8608 (p) REVERT: C 867 ASP cc_start: 0.7435 (t70) cc_final: 0.6991 (t0) REVERT: C 994 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6677 (mm-40) REVERT: C 1007 ILE cc_start: 0.7831 (pt) cc_final: 0.7599 (mm) REVERT: C 1041 SER cc_start: 0.8074 (m) cc_final: 0.7872 (t) REVERT: C 1065 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7132 (t0) REVERT: C 1135 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6991 (mm-30) outliers start: 73 outliers final: 32 residues processed: 547 average time/residue: 0.3494 time to fit residues: 307.1346 Evaluate side-chains 351 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 316 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 1145 PRO Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 723 ASN Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 1145 PRO Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 723 ASN Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1065 ASP Chi-restraints excluded: chain C residue 1154 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.7980 chunk 241 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 249 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 151 optimal weight: 0.5980 chunk 185 optimal weight: 0.5980 chunk 288 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 HIS A 707 ASN ** A 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN A 919 ASN A1040 ASN A1136 HIS B 292 GLN B 298 HIS B 507 HIS B 534 ASN B1136 HIS ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS C 507 HIS C 707 ASN C 822 GLN C1136 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 26013 Z= 0.333 Angle : 0.911 17.529 35445 Z= 0.430 Chirality : 0.066 1.299 4416 Planarity : 0.004 0.051 4419 Dihedral : 11.214 174.363 5150 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.92 % Allowed : 9.88 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3150 helix: -0.25 (0.19), residues: 630 sheet: 0.39 (0.18), residues: 711 loop : -0.80 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 256 HIS 0.004 0.001 HIS A1152 PHE 0.024 0.002 PHE B 371 TYR 0.027 0.002 TYR B 369 ARG 0.005 0.001 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 353 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7356 (m-80) cc_final: 0.7106 (m-80) REVERT: A 179 HIS cc_start: 0.7473 (m-70) cc_final: 0.6873 (m-70) REVERT: A 180 PHE cc_start: 0.7498 (m-80) cc_final: 0.7238 (m-80) REVERT: A 578 ASP cc_start: 0.7718 (t70) cc_final: 0.7497 (t70) REVERT: A 679 GLN cc_start: 0.7699 (tt0) cc_final: 0.7179 (mm110) REVERT: A 737 ASP cc_start: 0.7769 (t0) cc_final: 0.7364 (t0) REVERT: A 867 ASP cc_start: 0.7569 (t70) cc_final: 0.7110 (t0) REVERT: A 1027 THR cc_start: 0.8727 (t) cc_final: 0.8494 (t) REVERT: A 1068 TYR cc_start: 0.8411 (m-80) cc_final: 0.7854 (m-80) REVERT: A 1175 ILE cc_start: 0.7861 (pt) cc_final: 0.7526 (pt) REVERT: B 179 HIS cc_start: 0.7446 (m-70) cc_final: 0.7163 (m-70) REVERT: B 201 MET cc_start: 0.8140 (mmp) cc_final: 0.7541 (mmm) REVERT: B 284 ILE cc_start: 0.7772 (mm) cc_final: 0.7196 (mt) REVERT: B 450 VAL cc_start: 0.8508 (t) cc_final: 0.8252 (m) REVERT: B 566 ASP cc_start: 0.7579 (t0) cc_final: 0.7291 (t0) REVERT: B 578 ASP cc_start: 0.7853 (t0) cc_final: 0.7323 (t70) REVERT: B 583 SER cc_start: 0.8627 (t) cc_final: 0.8234 (p) REVERT: B 588 SER cc_start: 0.8604 (t) cc_final: 0.8328 (t) REVERT: B 635 ILE cc_start: 0.9122 (mm) cc_final: 0.8871 (mt) REVERT: B 701 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6827 (mt-10) REVERT: B 815 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7115 (ttp-170) REVERT: B 867 ASP cc_start: 0.7854 (t0) cc_final: 0.7481 (t0) REVERT: B 913 ASP cc_start: 0.8021 (p0) cc_final: 0.7718 (p0) REVERT: B 933 SER cc_start: 0.8562 (m) cc_final: 0.8165 (p) REVERT: B 1041 SER cc_start: 0.8611 (m) cc_final: 0.8363 (t) REVERT: B 1068 TYR cc_start: 0.8403 (m-80) cc_final: 0.8137 (m-80) REVERT: C 179 HIS cc_start: 0.7678 (OUTLIER) cc_final: 0.7226 (p90) REVERT: C 211 MET cc_start: 0.7004 (mtp) cc_final: 0.6802 (mtt) REVERT: C 284 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7374 (mt) REVERT: C 578 ASP cc_start: 0.7589 (t70) cc_final: 0.7109 (t0) REVERT: C 588 SER cc_start: 0.8354 (t) cc_final: 0.8112 (t) REVERT: C 679 GLN cc_start: 0.8157 (pt0) cc_final: 0.7925 (pt0) REVERT: C 737 ASP cc_start: 0.7518 (t0) cc_final: 0.7280 (t0) REVERT: C 745 VAL cc_start: 0.8775 (m) cc_final: 0.8554 (t) REVERT: C 867 ASP cc_start: 0.7653 (t70) cc_final: 0.7205 (t0) REVERT: C 1023 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8497 (mtpt) REVERT: C 1065 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.7047 (t0) outliers start: 80 outliers final: 46 residues processed: 417 average time/residue: 0.3361 time to fit residues: 228.6025 Evaluate side-chains 357 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 306 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 1203 SER Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 596 CYS Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1023 LYS Chi-restraints excluded: chain C residue 1065 ASP Chi-restraints excluded: chain C residue 1133 ASP Chi-restraints excluded: chain C residue 1222 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 240 optimal weight: 0.5980 chunk 196 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 289 optimal weight: 0.9980 chunk 312 optimal weight: 0.5980 chunk 257 optimal weight: 0.5980 chunk 286 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 HIS A 319 ASN A 426 HIS A 813 ASN A1048 GLN A1162 ASN B 534 ASN B1172 ASN C 298 HIS C 568 ASN C 822 GLN C 994 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 26013 Z= 0.301 Angle : 0.757 15.889 35445 Z= 0.363 Chirality : 0.055 0.670 4416 Planarity : 0.004 0.105 4419 Dihedral : 9.697 61.726 5115 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.38 % Allowed : 10.07 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3150 helix: 0.72 (0.21), residues: 612 sheet: 0.00 (0.19), residues: 651 loop : -0.67 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 256 HIS 0.004 0.001 HIS A1136 PHE 0.017 0.002 PHE C 640 TYR 0.015 0.002 TYR B1194 ARG 0.043 0.001 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 358 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7331 (m-80) cc_final: 0.6964 (m-80) REVERT: A 179 HIS cc_start: 0.7579 (m-70) cc_final: 0.7034 (m-70) REVERT: A 180 PHE cc_start: 0.7542 (m-80) cc_final: 0.7316 (m-80) REVERT: A 201 MET cc_start: 0.7048 (mmm) cc_final: 0.6846 (mmp) REVERT: A 567 SER cc_start: 0.8698 (m) cc_final: 0.8452 (p) REVERT: A 578 ASP cc_start: 0.7770 (t70) cc_final: 0.7566 (t70) REVERT: A 679 GLN cc_start: 0.7685 (tt0) cc_final: 0.7248 (mm110) REVERT: A 737 ASP cc_start: 0.7844 (t0) cc_final: 0.7565 (t0) REVERT: A 867 ASP cc_start: 0.7559 (t70) cc_final: 0.7008 (t0) REVERT: A 911 ASP cc_start: 0.7099 (p0) cc_final: 0.6887 (p0) REVERT: A 922 SER cc_start: 0.8934 (t) cc_final: 0.8688 (p) REVERT: A 943 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7566 (p0) REVERT: A 1175 ILE cc_start: 0.7868 (pt) cc_final: 0.7544 (pt) REVERT: B 180 PHE cc_start: 0.7532 (m-80) cc_final: 0.7195 (m-80) REVERT: B 181 TYR cc_start: 0.7268 (t80) cc_final: 0.6991 (t80) REVERT: B 201 MET cc_start: 0.8148 (mmp) cc_final: 0.7734 (mmm) REVERT: B 450 VAL cc_start: 0.8486 (t) cc_final: 0.8220 (m) REVERT: B 566 ASP cc_start: 0.7532 (t0) cc_final: 0.7234 (t0) REVERT: B 578 ASP cc_start: 0.7824 (t0) cc_final: 0.7248 (t70) REVERT: B 583 SER cc_start: 0.8620 (t) cc_final: 0.8220 (p) REVERT: B 588 SER cc_start: 0.8648 (t) cc_final: 0.8394 (t) REVERT: B 701 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6828 (mt-10) REVERT: B 815 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.6872 (ttp-170) REVERT: B 854 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8128 (pt0) REVERT: B 867 ASP cc_start: 0.7716 (t0) cc_final: 0.7292 (t0) REVERT: B 913 ASP cc_start: 0.7961 (p0) cc_final: 0.7713 (p0) REVERT: B 1027 THR cc_start: 0.8801 (t) cc_final: 0.8553 (t) REVERT: B 1068 TYR cc_start: 0.8446 (m-80) cc_final: 0.8172 (m-80) REVERT: C 211 MET cc_start: 0.7069 (mtp) cc_final: 0.6842 (mtt) REVERT: C 284 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7549 (mt) REVERT: C 487 ARG cc_start: 0.7662 (mmm-85) cc_final: 0.7437 (mtm180) REVERT: C 567 SER cc_start: 0.8450 (m) cc_final: 0.8184 (p) REVERT: C 578 ASP cc_start: 0.7704 (t70) cc_final: 0.7195 (t70) REVERT: C 588 SER cc_start: 0.8476 (t) cc_final: 0.8275 (t) REVERT: C 737 ASP cc_start: 0.7737 (t0) cc_final: 0.7528 (t0) REVERT: C 787 MET cc_start: 0.8520 (mtt) cc_final: 0.7965 (mtt) REVERT: C 867 ASP cc_start: 0.7607 (t70) cc_final: 0.7120 (t0) REVERT: C 922 SER cc_start: 0.8947 (t) cc_final: 0.8680 (p) outliers start: 120 outliers final: 75 residues processed: 451 average time/residue: 0.3289 time to fit residues: 244.5405 Evaluate side-chains 401 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 322 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1203 SER Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 596 CYS Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 716 SER Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 937 VAL Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1222 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.9980 chunk 217 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 32 optimal weight: 0.0770 chunk 138 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 290 optimal weight: 2.9990 chunk 307 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 chunk 275 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 813 ASN B 456 GLN C 298 HIS C 426 HIS C 822 GLN C 992 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26013 Z= 0.238 Angle : 0.673 15.451 35445 Z= 0.326 Chirality : 0.051 0.489 4416 Planarity : 0.004 0.048 4419 Dihedral : 8.917 59.880 5110 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.54 % Allowed : 12.80 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3150 helix: 1.15 (0.22), residues: 615 sheet: -0.42 (0.19), residues: 690 loop : -0.53 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.003 0.001 HIS C1136 PHE 0.019 0.001 PHE A 344 TYR 0.013 0.001 TYR B 234 ARG 0.004 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 342 time to evaluate : 3.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7281 (m-80) cc_final: 0.6841 (m-80) REVERT: A 179 HIS cc_start: 0.7545 (m-70) cc_final: 0.7025 (m-70) REVERT: A 201 MET cc_start: 0.7034 (mmm) cc_final: 0.6814 (mmp) REVERT: A 578 ASP cc_start: 0.7758 (t70) cc_final: 0.7434 (t70) REVERT: A 642 THR cc_start: 0.8705 (m) cc_final: 0.8486 (p) REVERT: A 679 GLN cc_start: 0.7749 (tt0) cc_final: 0.7354 (mm110) REVERT: A 737 ASP cc_start: 0.7849 (t0) cc_final: 0.7581 (t0) REVERT: A 841 GLU cc_start: 0.7678 (tp30) cc_final: 0.7427 (tp30) REVERT: A 867 ASP cc_start: 0.7509 (t70) cc_final: 0.6983 (t0) REVERT: A 911 ASP cc_start: 0.7137 (p0) cc_final: 0.6794 (p0) REVERT: A 922 SER cc_start: 0.8964 (t) cc_final: 0.8689 (p) REVERT: A 943 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7648 (p0) REVERT: B 180 PHE cc_start: 0.7578 (m-80) cc_final: 0.7349 (m-80) REVERT: B 450 VAL cc_start: 0.8488 (t) cc_final: 0.8242 (m) REVERT: B 566 ASP cc_start: 0.7610 (t0) cc_final: 0.7336 (t0) REVERT: B 578 ASP cc_start: 0.7828 (t0) cc_final: 0.7177 (t70) REVERT: B 583 SER cc_start: 0.8621 (t) cc_final: 0.8173 (p) REVERT: B 588 SER cc_start: 0.8663 (t) cc_final: 0.8414 (t) REVERT: B 599 ASP cc_start: 0.7353 (m-30) cc_final: 0.7117 (m-30) REVERT: B 854 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8113 (pt0) REVERT: B 867 ASP cc_start: 0.7697 (t0) cc_final: 0.7261 (t0) REVERT: B 1068 TYR cc_start: 0.8427 (m-80) cc_final: 0.8028 (m-80) REVERT: C 182 LEU cc_start: 0.6985 (mt) cc_final: 0.6781 (mt) REVERT: C 284 ILE cc_start: 0.7689 (mm) cc_final: 0.7475 (mt) REVERT: C 540 CYS cc_start: 0.6441 (OUTLIER) cc_final: 0.6234 (p) REVERT: C 578 ASP cc_start: 0.7725 (t70) cc_final: 0.7146 (t70) REVERT: C 737 ASP cc_start: 0.7762 (t0) cc_final: 0.7541 (t0) REVERT: C 867 ASP cc_start: 0.7591 (t70) cc_final: 0.7082 (t0) REVERT: C 922 SER cc_start: 0.8964 (t) cc_final: 0.8714 (p) REVERT: C 1041 SER cc_start: 0.8215 (t) cc_final: 0.7975 (p) outliers start: 97 outliers final: 67 residues processed: 420 average time/residue: 0.3315 time to fit residues: 229.1661 Evaluate side-chains 382 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 312 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 1034 LYS Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 540 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 716 SER Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 937 VAL Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1222 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 228 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 156 optimal weight: 0.0970 chunk 275 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 813 ASN B 305 ASN B1162 ASN C 298 HIS C 305 ASN C 822 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 26013 Z= 0.274 Angle : 0.647 13.036 35445 Z= 0.318 Chirality : 0.050 0.464 4416 Planarity : 0.004 0.047 4419 Dihedral : 8.387 58.646 5102 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.30 % Allowed : 12.76 % Favored : 82.93 % 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: -0.26 (0.15), residues: 3150 helix: 1.21 (0.22), residues: 621 sheet: -0.29 (0.19), residues: 642 loop : -0.57 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 256 HIS 0.003 0.001 HIS B1136 PHE 0.018 0.002 PHE C 344 TYR 0.014 0.001 TYR B 234 ARG 0.002 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 336 time to evaluate : 3.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7382 (m-80) cc_final: 0.6990 (m-80) REVERT: A 179 HIS cc_start: 0.7588 (m-70) cc_final: 0.6994 (m-70) REVERT: A 201 MET cc_start: 0.7005 (mmm) cc_final: 0.6768 (mmp) REVERT: A 578 ASP cc_start: 0.7815 (t70) cc_final: 0.7468 (t70) REVERT: A 679 GLN cc_start: 0.7753 (tt0) cc_final: 0.7369 (mm110) REVERT: A 841 GLU cc_start: 0.7666 (tp30) cc_final: 0.7461 (tp30) REVERT: A 867 ASP cc_start: 0.7508 (t70) cc_final: 0.6965 (t0) REVERT: A 911 ASP cc_start: 0.6919 (p0) cc_final: 0.6636 (p0) REVERT: A 922 SER cc_start: 0.8993 (t) cc_final: 0.8732 (p) REVERT: A 943 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7731 (p0) REVERT: B 180 PHE cc_start: 0.7565 (m-80) cc_final: 0.7349 (m-80) REVERT: B 201 MET cc_start: 0.8071 (mmp) cc_final: 0.7601 (mmm) REVERT: B 284 ILE cc_start: 0.7846 (mm) cc_final: 0.7524 (mt) REVERT: B 450 VAL cc_start: 0.8494 (t) cc_final: 0.8264 (m) REVERT: B 566 ASP cc_start: 0.7629 (t0) cc_final: 0.7352 (t0) REVERT: B 578 ASP cc_start: 0.7844 (t0) cc_final: 0.7141 (t70) REVERT: B 588 SER cc_start: 0.8660 (t) cc_final: 0.8423 (t) REVERT: B 599 ASP cc_start: 0.7345 (m-30) cc_final: 0.7108 (m-30) REVERT: B 854 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8115 (pt0) REVERT: B 867 ASP cc_start: 0.7703 (t0) cc_final: 0.7266 (t0) REVERT: B 1068 TYR cc_start: 0.8434 (m-80) cc_final: 0.8045 (m-80) REVERT: C 211 MET cc_start: 0.7068 (mtp) cc_final: 0.6712 (mtp) REVERT: C 284 ILE cc_start: 0.7686 (mm) cc_final: 0.7479 (mt) REVERT: C 311 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7927 (mtm180) REVERT: C 526 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8185 (tt) REVERT: C 578 ASP cc_start: 0.7754 (t70) cc_final: 0.7149 (t70) REVERT: C 586 CYS cc_start: 0.5858 (m) cc_final: 0.5643 (m) REVERT: C 867 ASP cc_start: 0.7594 (t70) cc_final: 0.7069 (t0) REVERT: C 922 SER cc_start: 0.8964 (t) cc_final: 0.8703 (p) REVERT: C 1036 GLN cc_start: 0.7479 (mt0) cc_final: 0.7117 (mt0) REVERT: C 1041 SER cc_start: 0.8236 (t) cc_final: 0.8025 (p) outliers start: 118 outliers final: 94 residues processed: 432 average time/residue: 0.3283 time to fit residues: 233.5642 Evaluate side-chains 409 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 311 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1034 LYS Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1034 LYS Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 540 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 716 SER Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 937 VAL Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1137 ILE Chi-restraints excluded: chain C residue 1222 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.9980 chunk 276 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 180 optimal weight: 0.0980 chunk 75 optimal weight: 0.0020 chunk 307 optimal weight: 0.9980 chunk 255 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 813 ASN A1048 GLN B 305 ASN B1042 GLN B1146 GLN C 298 HIS C 305 ASN C 822 GLN C 873 ASN C1048 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 26013 Z= 0.239 Angle : 0.623 13.641 35445 Z= 0.307 Chirality : 0.049 0.497 4416 Planarity : 0.003 0.044 4419 Dihedral : 7.995 57.662 5099 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.34 % Allowed : 13.86 % Favored : 81.80 % 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: 3150 helix: 1.29 (0.22), residues: 630 sheet: -0.49 (0.19), residues: 672 loop : -0.50 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 256 HIS 0.003 0.001 HIS A 335 PHE 0.022 0.001 PHE C 344 TYR 0.018 0.001 TYR C 209 ARG 0.003 0.000 ARG B 393 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 331 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7404 (m-80) cc_final: 0.7043 (m-80) REVERT: A 179 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.7007 (m-70) REVERT: A 244 ASN cc_start: 0.7225 (m-40) cc_final: 0.6898 (t0) REVERT: A 578 ASP cc_start: 0.7720 (t70) cc_final: 0.7313 (t70) REVERT: A 638 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8185 (p) REVERT: A 679 GLN cc_start: 0.7761 (tt0) cc_final: 0.7389 (mm110) REVERT: A 867 ASP cc_start: 0.7501 (t70) cc_final: 0.6946 (t0) REVERT: A 911 ASP cc_start: 0.6917 (p0) cc_final: 0.6644 (p0) REVERT: A 922 SER cc_start: 0.8984 (t) cc_final: 0.8720 (p) REVERT: A 943 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7709 (p0) REVERT: A 1066 ASP cc_start: 0.7940 (t0) cc_final: 0.7577 (t0) REVERT: B 180 PHE cc_start: 0.7469 (m-80) cc_final: 0.7243 (m-80) REVERT: B 201 MET cc_start: 0.8063 (mmp) cc_final: 0.7596 (mmm) REVERT: B 284 ILE cc_start: 0.7857 (mm) cc_final: 0.7541 (mt) REVERT: B 349 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8713 (p) REVERT: B 450 VAL cc_start: 0.8506 (t) cc_final: 0.8277 (m) REVERT: B 566 ASP cc_start: 0.7648 (t0) cc_final: 0.7395 (t0) REVERT: B 578 ASP cc_start: 0.7839 (t0) cc_final: 0.7099 (t70) REVERT: B 588 SER cc_start: 0.8674 (t) cc_final: 0.8446 (t) REVERT: B 599 ASP cc_start: 0.7346 (m-30) cc_final: 0.7101 (m-30) REVERT: B 638 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8381 (p) REVERT: B 854 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8092 (pt0) REVERT: B 867 ASP cc_start: 0.7709 (t0) cc_final: 0.7226 (t0) REVERT: B 1068 TYR cc_start: 0.8429 (m-80) cc_final: 0.8052 (m-80) REVERT: C 211 MET cc_start: 0.7101 (mtp) cc_final: 0.6753 (mtp) REVERT: C 526 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8180 (tt) REVERT: C 578 ASP cc_start: 0.7751 (t70) cc_final: 0.7088 (t70) REVERT: C 867 ASP cc_start: 0.7591 (t70) cc_final: 0.7059 (t0) REVERT: C 922 SER cc_start: 0.8962 (t) cc_final: 0.8702 (p) REVERT: C 1036 GLN cc_start: 0.7476 (mt0) cc_final: 0.7089 (mt0) REVERT: C 1041 SER cc_start: 0.8321 (t) cc_final: 0.8089 (p) outliers start: 119 outliers final: 88 residues processed: 426 average time/residue: 0.3216 time to fit residues: 226.4265 Evaluate side-chains 406 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 311 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1034 LYS Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1154 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 540 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 716 SER Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 937 VAL Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1137 ILE Chi-restraints excluded: chain C residue 1222 SER Chi-restraints excluded: chain C residue 1226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 224 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 259 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 306 optimal weight: 0.9980 chunk 191 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 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 298 HIS A 813 ASN A1048 GLN B 707 ASN B 873 ASN C 298 HIS C 305 ASN C 822 GLN C1048 GLN C1125 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 26013 Z= 0.334 Angle : 0.647 12.995 35445 Z= 0.320 Chirality : 0.051 0.614 4416 Planarity : 0.004 0.044 4419 Dihedral : 7.904 59.565 5099 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 4.49 % Allowed : 14.22 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3150 helix: 1.26 (0.22), residues: 630 sheet: -0.60 (0.19), residues: 693 loop : -0.54 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 256 HIS 0.004 0.001 HIS B1136 PHE 0.016 0.002 PHE A 344 TYR 0.018 0.001 TYR B 209 ARG 0.006 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 322 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7454 (m-80) cc_final: 0.7057 (m-80) REVERT: A 179 HIS cc_start: 0.7565 (OUTLIER) cc_final: 0.7008 (m-70) REVERT: A 244 ASN cc_start: 0.7348 (m-40) cc_final: 0.6966 (t0) REVERT: A 578 ASP cc_start: 0.7763 (t70) cc_final: 0.7356 (t70) REVERT: A 679 GLN cc_start: 0.7756 (tt0) cc_final: 0.7374 (mm110) REVERT: A 867 ASP cc_start: 0.7501 (t70) cc_final: 0.6927 (t0) REVERT: A 911 ASP cc_start: 0.6943 (p0) cc_final: 0.6669 (p0) REVERT: A 943 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7769 (p0) REVERT: A 1066 ASP cc_start: 0.7963 (t0) cc_final: 0.7626 (t0) REVERT: B 180 PHE cc_start: 0.7508 (m-80) cc_final: 0.7304 (m-80) REVERT: B 284 ILE cc_start: 0.7882 (mm) cc_final: 0.7605 (mt) REVERT: B 349 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8807 (p) REVERT: B 450 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8305 (m) REVERT: B 566 ASP cc_start: 0.7654 (t0) cc_final: 0.7441 (t0) REVERT: B 578 ASP cc_start: 0.7852 (t0) cc_final: 0.7112 (t70) REVERT: B 588 SER cc_start: 0.8671 (t) cc_final: 0.8444 (t) REVERT: B 591 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8368 (tt) REVERT: B 599 ASP cc_start: 0.7358 (m-30) cc_final: 0.7109 (m-30) REVERT: B 638 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8421 (p) REVERT: B 854 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8101 (pt0) REVERT: B 867 ASP cc_start: 0.7706 (t0) cc_final: 0.7225 (t0) REVERT: B 1068 TYR cc_start: 0.8497 (m-80) cc_final: 0.8145 (m-80) REVERT: C 277 LEU cc_start: 0.8464 (tp) cc_final: 0.8234 (tp) REVERT: C 574 GLN cc_start: 0.8396 (pm20) cc_final: 0.7975 (mp10) REVERT: C 578 ASP cc_start: 0.7758 (t70) cc_final: 0.7091 (t70) REVERT: C 867 ASP cc_start: 0.7596 (t70) cc_final: 0.7064 (t0) REVERT: C 1036 GLN cc_start: 0.7491 (mt0) cc_final: 0.7107 (mt0) REVERT: C 1041 SER cc_start: 0.8322 (t) cc_final: 0.8042 (p) outliers start: 123 outliers final: 98 residues processed: 420 average time/residue: 0.3300 time to fit residues: 229.8389 Evaluate side-chains 413 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 308 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1034 LYS Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1034 LYS Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1154 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 488 ASN Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 716 SER Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 937 VAL Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1137 ILE Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1222 SER Chi-restraints excluded: chain C residue 1226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 194 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 151 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 240 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 813 ASN A1048 GLN C 822 GLN C1048 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 26013 Z= 0.271 Angle : 0.626 15.329 35445 Z= 0.309 Chirality : 0.049 0.483 4416 Planarity : 0.003 0.044 4419 Dihedral : 7.681 59.040 5099 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 4.16 % Allowed : 14.92 % Favored : 80.93 % 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: -0.28 (0.15), residues: 3150 helix: 1.37 (0.22), residues: 627 sheet: -0.57 (0.19), residues: 675 loop : -0.54 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 165 HIS 0.003 0.001 HIS A1136 PHE 0.016 0.001 PHE A 344 TYR 0.019 0.001 TYR C 209 ARG 0.006 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 323 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7476 (m-80) cc_final: 0.7133 (m-80) REVERT: A 179 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.7060 (m-70) REVERT: A 244 ASN cc_start: 0.7278 (m-40) cc_final: 0.6968 (t0) REVERT: A 297 ASN cc_start: 0.7084 (OUTLIER) cc_final: 0.6820 (t0) REVERT: A 578 ASP cc_start: 0.7753 (t70) cc_final: 0.7327 (t70) REVERT: A 679 GLN cc_start: 0.7754 (tt0) cc_final: 0.7378 (mm110) REVERT: A 867 ASP cc_start: 0.7494 (t70) cc_final: 0.6913 (t0) REVERT: A 911 ASP cc_start: 0.6950 (p0) cc_final: 0.6734 (p0) REVERT: A 943 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7754 (p0) REVERT: A 1066 ASP cc_start: 0.7942 (t0) cc_final: 0.7661 (t0) REVERT: B 201 MET cc_start: 0.8004 (mmp) cc_final: 0.7464 (mmm) REVERT: B 211 MET cc_start: 0.6809 (mtt) cc_final: 0.6526 (mmt) REVERT: B 284 ILE cc_start: 0.7898 (mm) cc_final: 0.7630 (mt) REVERT: B 349 SER cc_start: 0.9050 (OUTLIER) cc_final: 0.8831 (p) REVERT: B 450 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8314 (m) REVERT: B 566 ASP cc_start: 0.7649 (t0) cc_final: 0.7435 (t0) REVERT: B 578 ASP cc_start: 0.7932 (t0) cc_final: 0.7136 (t70) REVERT: B 588 SER cc_start: 0.8654 (t) cc_final: 0.8434 (t) REVERT: B 599 ASP cc_start: 0.7359 (m-30) cc_final: 0.7112 (m-30) REVERT: B 854 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8078 (pt0) REVERT: B 867 ASP cc_start: 0.7753 (t0) cc_final: 0.7289 (t0) REVERT: B 1068 TYR cc_start: 0.8478 (m-80) cc_final: 0.8131 (m-80) REVERT: C 526 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8278 (tt) REVERT: C 574 GLN cc_start: 0.8420 (pm20) cc_final: 0.8209 (mp10) REVERT: C 578 ASP cc_start: 0.7760 (t70) cc_final: 0.7085 (t70) REVERT: C 743 GLU cc_start: 0.7184 (pm20) cc_final: 0.6951 (pm20) REVERT: C 867 ASP cc_start: 0.7589 (t70) cc_final: 0.7052 (t0) REVERT: C 1041 SER cc_start: 0.8311 (t) cc_final: 0.8101 (p) REVERT: C 1216 ASP cc_start: 0.7803 (m-30) cc_final: 0.7548 (m-30) outliers start: 114 outliers final: 98 residues processed: 414 average time/residue: 0.3353 time to fit residues: 229.4526 Evaluate side-chains 414 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 309 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1034 LYS Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1034 LYS Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1154 VAL Chi-restraints excluded: chain B residue 1161 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 488 ASN Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 540 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 716 SER Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 937 VAL Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1137 ILE Chi-restraints excluded: chain C residue 1222 SER Chi-restraints excluded: chain C residue 1226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.9980 chunk 293 optimal weight: 0.9980 chunk 267 optimal weight: 0.9980 chunk 285 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 224 optimal weight: 0.0770 chunk 87 optimal weight: 0.9980 chunk 258 optimal weight: 1.9990 chunk 270 optimal weight: 0.6980 chunk 284 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 813 ASN A 994 GLN B 456 GLN C 822 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 26013 Z= 0.316 Angle : 0.638 14.776 35445 Z= 0.315 Chirality : 0.050 0.416 4416 Planarity : 0.004 0.042 4419 Dihedral : 7.642 58.341 5099 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 4.30 % Allowed : 14.92 % Favored : 80.78 % 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: -0.27 (0.15), residues: 3150 helix: 1.36 (0.22), residues: 627 sheet: -0.55 (0.19), residues: 717 loop : -0.53 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.004 0.001 HIS A1136 PHE 0.021 0.002 PHE B 344 TYR 0.017 0.001 TYR C 209 ARG 0.006 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 313 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7502 (m-80) cc_final: 0.7153 (m-80) REVERT: A 179 HIS cc_start: 0.7526 (OUTLIER) cc_final: 0.7030 (m-70) REVERT: A 244 ASN cc_start: 0.7310 (m-40) cc_final: 0.7017 (t0) REVERT: A 297 ASN cc_start: 0.7101 (OUTLIER) cc_final: 0.6839 (t0) REVERT: A 578 ASP cc_start: 0.7765 (t70) cc_final: 0.7345 (t70) REVERT: A 679 GLN cc_start: 0.7760 (tt0) cc_final: 0.7377 (mm110) REVERT: A 867 ASP cc_start: 0.7497 (t70) cc_final: 0.6913 (t0) REVERT: A 911 ASP cc_start: 0.6928 (p0) cc_final: 0.6715 (p0) REVERT: A 943 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7780 (p0) REVERT: A 1066 ASP cc_start: 0.7946 (t0) cc_final: 0.7672 (t0) REVERT: B 201 MET cc_start: 0.8035 (mmp) cc_final: 0.7490 (mmm) REVERT: B 284 ILE cc_start: 0.7909 (mm) cc_final: 0.7639 (mt) REVERT: B 450 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8296 (m) REVERT: B 578 ASP cc_start: 0.7845 (t0) cc_final: 0.7097 (t70) REVERT: B 599 ASP cc_start: 0.7371 (m-30) cc_final: 0.7125 (m-30) REVERT: B 854 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8015 (pt0) REVERT: B 867 ASP cc_start: 0.7728 (t0) cc_final: 0.7262 (t0) REVERT: B 913 ASP cc_start: 0.8152 (p0) cc_final: 0.7893 (p0) REVERT: B 1068 TYR cc_start: 0.8487 (m-80) cc_final: 0.8138 (m-80) REVERT: C 211 MET cc_start: 0.7081 (mtp) cc_final: 0.6837 (mtp) REVERT: C 298 HIS cc_start: 0.8401 (m170) cc_final: 0.8141 (m170) REVERT: C 526 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8281 (tt) REVERT: C 578 ASP cc_start: 0.7762 (t70) cc_final: 0.7131 (t70) REVERT: C 743 GLU cc_start: 0.7197 (pm20) cc_final: 0.6928 (pm20) REVERT: C 867 ASP cc_start: 0.7596 (t70) cc_final: 0.7032 (t0) REVERT: C 1036 GLN cc_start: 0.7509 (mt0) cc_final: 0.7119 (mt0) REVERT: C 1041 SER cc_start: 0.8339 (t) cc_final: 0.8114 (p) REVERT: C 1216 ASP cc_start: 0.7821 (m-30) cc_final: 0.7554 (m-30) outliers start: 118 outliers final: 97 residues processed: 409 average time/residue: 0.3352 time to fit residues: 228.2020 Evaluate side-chains 405 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 302 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1034 LYS Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1154 VAL Chi-restraints excluded: chain B residue 1161 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 488 ASN Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 540 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 716 SER Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 THR Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 937 VAL Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1137 ILE Chi-restraints excluded: chain C residue 1222 SER Chi-restraints excluded: chain C residue 1226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.6980 chunk 302 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 143 optimal weight: 0.3980 chunk 209 optimal weight: 0.7980 chunk 316 optimal weight: 0.7980 chunk 291 optimal weight: 0.0010 chunk 252 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 813 ASN B 426 HIS B 456 GLN C 822 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 26013 Z= 0.243 Angle : 0.616 14.378 35445 Z= 0.306 Chirality : 0.049 0.583 4416 Planarity : 0.003 0.044 4419 Dihedral : 7.496 59.535 5099 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.86 % Rotamer: Outliers : 3.68 % Allowed : 15.79 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3150 helix: 1.50 (0.22), residues: 627 sheet: -0.55 (0.19), residues: 717 loop : -0.50 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 165 HIS 0.003 0.001 HIS A 335 PHE 0.017 0.001 PHE B 344 TYR 0.017 0.001 TYR C 209 ARG 0.006 0.000 ARG A 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 312 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7436 (m-80) cc_final: 0.7081 (m-80) REVERT: A 179 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.7054 (m-70) REVERT: A 244 ASN cc_start: 0.7291 (m-40) cc_final: 0.7021 (t0) REVERT: A 297 ASN cc_start: 0.7149 (OUTLIER) cc_final: 0.6874 (t0) REVERT: A 506 ASP cc_start: 0.7288 (t0) cc_final: 0.7066 (t70) REVERT: A 578 ASP cc_start: 0.7819 (t70) cc_final: 0.7391 (t70) REVERT: A 679 GLN cc_start: 0.7748 (tt0) cc_final: 0.7378 (mm110) REVERT: A 867 ASP cc_start: 0.7492 (t70) cc_final: 0.6904 (t0) REVERT: A 911 ASP cc_start: 0.6898 (p0) cc_final: 0.6698 (p0) REVERT: A 1066 ASP cc_start: 0.7916 (t0) cc_final: 0.7669 (t0) REVERT: B 201 MET cc_start: 0.8010 (mmp) cc_final: 0.7460 (mmm) REVERT: B 284 ILE cc_start: 0.7899 (mm) cc_final: 0.7648 (mt) REVERT: B 450 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8263 (m) REVERT: B 578 ASP cc_start: 0.7880 (t0) cc_final: 0.7105 (t70) REVERT: B 599 ASP cc_start: 0.7337 (m-30) cc_final: 0.7111 (m-30) REVERT: B 854 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8050 (pt0) REVERT: B 867 ASP cc_start: 0.7725 (t0) cc_final: 0.7249 (t0) REVERT: B 1068 TYR cc_start: 0.8468 (m-80) cc_final: 0.8124 (m-80) REVERT: C 211 MET cc_start: 0.7082 (mtp) cc_final: 0.6869 (mtp) REVERT: C 298 HIS cc_start: 0.8387 (m170) cc_final: 0.8092 (m170) REVERT: C 526 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8252 (tt) REVERT: C 578 ASP cc_start: 0.7752 (t70) cc_final: 0.7079 (t70) REVERT: C 867 ASP cc_start: 0.7586 (t70) cc_final: 0.7007 (t0) REVERT: C 1041 SER cc_start: 0.8367 (t) cc_final: 0.8149 (p) REVERT: C 1216 ASP cc_start: 0.7816 (m-30) cc_final: 0.7551 (m-30) outliers start: 101 outliers final: 89 residues processed: 395 average time/residue: 0.3663 time to fit residues: 240.7372 Evaluate side-chains 395 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 301 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1034 LYS Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1154 VAL Chi-restraints excluded: chain B residue 1161 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 488 ASN Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 596 CYS Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 716 SER Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 THR Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 937 VAL Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1137 ILE Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1222 SER Chi-restraints excluded: chain C residue 1226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.2980 chunk 268 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 232 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 252 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 259 optimal weight: 0.9980 chunk 31 optimal weight: 0.0270 chunk 46 optimal weight: 0.6980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 813 ASN B 456 GLN B 707 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.092860 restraints weight = 38860.621| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.42 r_work: 0.3085 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 26013 Z= 0.225 Angle : 0.597 14.195 35445 Z= 0.297 Chirality : 0.048 0.526 4416 Planarity : 0.003 0.045 4419 Dihedral : 7.269 58.545 5099 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.14 % Favored : 96.76 % Rotamer: Outliers : 3.43 % Allowed : 15.94 % Favored : 80.63 % 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: -0.17 (0.15), residues: 3150 helix: 1.58 (0.22), residues: 627 sheet: -0.57 (0.19), residues: 717 loop : -0.47 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 165 HIS 0.003 0.001 HIS A 335 PHE 0.025 0.001 PHE C 344 TYR 0.016 0.001 TYR C 209 ARG 0.006 0.000 ARG A 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6062.07 seconds wall clock time: 110 minutes 51.39 seconds (6651.39 seconds total)