Starting phenix.real_space_refine on Sat Dec 16 12:47:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v85_31790/12_2023/7v85_31790.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v85_31790/12_2023/7v85_31790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v85_31790/12_2023/7v85_31790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v85_31790/12_2023/7v85_31790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v85_31790/12_2023/7v85_31790.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v85_31790/12_2023/7v85_31790.pdb" } resolution = 3.3 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= 0.040 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 169 5.16 5 C 22353 2.51 5 N 5738 2.21 5 O 6841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 499": "OD1" <-> "OD2" Residue "F TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35101 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "B" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "C" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "H" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 16.50, per 1000 atoms: 0.47 Number of scatterers: 35101 At special positions: 0 Unit cell: (177.1, 158.4, 240.9, 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 169 16.00 O 6841 8.00 N 5738 7.00 C 22353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 141 " distance=2.02 Simple disulfide: pdb=" SG CYS H 344 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 530 " - pdb=" SG CYS H 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 234 " " NAG A2003 " - " ASN A 603 " " NAG A2004 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 603 " " NAG B2004 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 165 " " NAG C2003 " - " ASN C 234 " " NAG C2004 " - " ASN C 603 " " NAG C2005 " - " ASN C 657 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 331 " " NAG J 1 " - " ASN A 616 " " NAG K 1 " - " ASN A 709 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG S 1 " - " ASN B 282 " " NAG T 1 " - " ASN B 331 " " NAG U 1 " - " ASN B 616 " " NAG V 1 " - " ASN B 709 " " NAG W 1 " - " ASN B 717 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B1074 " " NAG Z 1 " - " ASN B1098 " " NAG a 1 " - " ASN B1134 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 282 " " NAG d 1 " - " ASN C 616 " " NAG e 1 " - " ASN C 709 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 14.90 Conformation dependent library (CDL) restraints added in 5.8 seconds 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8088 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 52 sheets defined 34.8% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.750A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.520A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.983A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.604A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.550A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.808A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.611A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.952A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.244A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.590A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.158A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.944A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.092A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.501A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.205A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.662A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.137A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.617A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.197A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.671A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.023A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.929A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.706A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.297A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.870A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 79 removed outlier: 3.656A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 101 removed outlier: 3.646A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 152 Processing helix chain 'F' and resid 157 through 171 removed outlier: 3.573A pdb=" N ARG F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 194 Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 221 through 231 removed outlier: 3.749A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 250 removed outlier: 3.931A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 281 removed outlier: 4.199A pdb=" N SER F 280 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.641A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.565A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 412 removed outlier: 4.207A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.588A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 466 removed outlier: 4.477A pdb=" N PHE F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 484 removed outlier: 3.736A pdb=" N TRP F 477 " --> pdb=" O TRP F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 512 through 532 removed outlier: 4.549A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.596A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.948A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 removed outlier: 4.018A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 53 removed outlier: 3.740A pdb=" N HIS H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP H 38 " --> pdb=" O HIS H 34 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU H 39 " --> pdb=" O GLU H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 80 removed outlier: 3.556A pdb=" N VAL H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER H 70 " --> pdb=" O GLY H 66 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 101 removed outlier: 4.004A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 147 through 154 Processing helix chain 'H' and resid 157 through 172 removed outlier: 3.999A pdb=" N ARG H 161 " --> pdb=" O ASP H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 194 removed outlier: 4.517A pdb=" N LEU H 179 " --> pdb=" O GLN H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 205 Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 220 through 231 removed outlier: 3.939A pdb=" N GLU H 224 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 251 Processing helix chain 'H' and resid 279 through 283 removed outlier: 3.742A pdb=" N VAL H 283 " --> pdb=" O SER H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 301 Processing helix chain 'H' and resid 303 through 319 Processing helix chain 'H' and resid 326 through 331 removed outlier: 3.629A pdb=" N SER H 331 " --> pdb=" O PHE H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 385 removed outlier: 3.558A pdb=" N TYR H 385 " --> pdb=" O TYR H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 389 through 393 removed outlier: 3.573A pdb=" N ARG H 393 " --> pdb=" O PHE H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 398 through 412 removed outlier: 4.514A pdb=" N GLU H 402 " --> pdb=" O GLU H 398 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER H 409 " --> pdb=" O GLY H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 421 removed outlier: 3.628A pdb=" N LEU H 418 " --> pdb=" O THR H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 447 removed outlier: 3.510A pdb=" N GLU H 435 " --> pdb=" O ASP H 431 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR H 445 " --> pdb=" O LYS H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 466 Processing helix chain 'H' and resid 473 through 484 Processing helix chain 'H' and resid 503 through 508 Processing helix chain 'H' and resid 512 through 532 removed outlier: 3.809A pdb=" N TYR H 516 " --> pdb=" O PHE H 512 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU H 520 " --> pdb=" O TYR H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 542 Processing helix chain 'H' and resid 547 through 559 Processing helix chain 'H' and resid 560 through 564 removed outlier: 4.224A pdb=" N GLU H 564 " --> pdb=" O GLY H 561 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 570 Processing helix chain 'H' and resid 581 through 588 removed outlier: 3.591A pdb=" N LEU H 585 " --> pdb=" O VAL H 581 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE H 588 " --> pdb=" O LEU H 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 588 through 599 removed outlier: 3.501A pdb=" N PHE H 592 " --> pdb=" O PHE H 588 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP H 597 " --> pdb=" O THR H 593 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN H 599 " --> pdb=" O LEU H 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.205A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.917A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.523A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 144 removed outlier: 5.552A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.685A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.450A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 7.428A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.927A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.994A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.407A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.662A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.912A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB8, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.896A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.848A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.885A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.711A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.711A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 143 through 144 removed outlier: 6.149A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.409A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.022A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.592A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.680A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.008A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.535A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.397A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.489A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.768A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.556A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.899A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.783A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.282A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 134 through 135 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.291A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.922A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 566 through 567 removed outlier: 6.648A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.123A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.549A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.487A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.557A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AF5, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AF6, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AF7, first strand: chain 'H' and resid 347 through 349 1466 hydrogen bonds defined for protein. 4098 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: 15.32 Time building geometry restraints manager: 15.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10922 1.34 - 1.46: 7345 1.46 - 1.58: 17427 1.58 - 1.70: 1 1.70 - 1.82: 238 Bond restraints: 35933 Sorted by residual: bond pdb=" CB PRO B 26 " pdb=" CG PRO B 26 " ideal model delta sigma weight residual 1.492 1.610 -0.118 5.00e-02 4.00e+02 5.55e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.361 0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" C1 NAG h 1 " pdb=" O5 NAG h 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.65e+00 bond pdb=" C CYS B 617 " pdb=" N THR B 618 " ideal model delta sigma weight residual 1.332 1.304 0.029 1.40e-02 5.10e+03 4.24e+00 bond pdb=" C1 NAG Y 1 " pdb=" C2 NAG Y 1 " ideal model delta sigma weight residual 1.532 1.494 0.038 2.00e-02 2.50e+03 3.56e+00 ... (remaining 35928 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.45: 582 104.45 - 111.84: 17367 111.84 - 119.23: 11856 119.23 - 126.62: 18562 126.62 - 134.01: 515 Bond angle restraints: 48882 Sorted by residual: angle pdb=" CA PRO B 26 " pdb=" N PRO B 26 " pdb=" CD PRO B 26 " ideal model delta sigma weight residual 112.00 104.70 7.30 1.40e+00 5.10e-01 2.72e+01 angle pdb=" C GLN F 89 " pdb=" N ASN F 90 " pdb=" CA ASN F 90 " ideal model delta sigma weight residual 121.54 131.47 -9.93 1.91e+00 2.74e-01 2.70e+01 angle pdb=" N PRO B 26 " pdb=" CD PRO B 26 " pdb=" CG PRO B 26 " ideal model delta sigma weight residual 103.20 97.29 5.91 1.50e+00 4.44e-01 1.55e+01 angle pdb=" N GLN B1002 " pdb=" CA GLN B1002 " pdb=" CB GLN B1002 " ideal model delta sigma weight residual 110.12 115.62 -5.50 1.47e+00 4.63e-01 1.40e+01 angle pdb=" CA LEU A 560 " pdb=" CB LEU A 560 " pdb=" CG LEU A 560 " ideal model delta sigma weight residual 116.30 129.35 -13.05 3.50e+00 8.16e-02 1.39e+01 ... (remaining 48877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 19998 17.80 - 35.60: 1836 35.60 - 53.40: 339 53.40 - 71.19: 103 71.19 - 88.99: 42 Dihedral angle restraints: 22318 sinusoidal: 9753 harmonic: 12565 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 179.77 -86.77 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 177.44 -84.44 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -168.16 82.16 1 1.00e+01 1.00e-02 8.29e+01 ... (remaining 22315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 5634 0.214 - 0.427: 7 0.427 - 0.641: 1 0.641 - 0.854: 1 0.854 - 1.068: 2 Chirality restraints: 5645 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.36e+01 ... (remaining 5642 not shown) Planarity restraints: 6272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " -0.022 2.00e-02 2.50e+03 2.01e-02 5.06e+00 pdb=" CG ASN C 165 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " 0.022 2.00e-02 2.50e+03 pdb=" C1 NAG C2002 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 89 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C GLN F 89 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN F 89 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN F 90 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO A 986 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.028 5.00e-02 4.00e+02 ... (remaining 6269 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 816 2.67 - 3.23: 34785 3.23 - 3.78: 54627 3.78 - 4.34: 70860 4.34 - 4.90: 116349 Nonbonded interactions: 277437 Sorted by model distance: nonbonded pdb=" OE2 GLU B 725 " pdb=" NE2 HIS B1064 " model vdw 2.111 2.520 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.135 2.440 nonbonded pdb=" OD1 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 2.136 2.440 nonbonded pdb=" OG SER C 349 " pdb=" O ARG C 452 " model vdw 2.139 2.440 nonbonded pdb=" O TYR H 215 " pdb=" OG1 THR H 567 " model vdw 2.144 2.440 ... (remaining 277432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 14 through 1146 or resid 2001 through 2004)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 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: 13.750 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 89.240 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.690 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 35933 Z= 0.329 Angle : 0.665 13.049 48882 Z= 0.341 Chirality : 0.052 1.068 5645 Planarity : 0.004 0.051 6228 Dihedral : 14.309 88.993 14098 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.75 % Favored : 93.16 % Rotamer: Outliers : 0.03 % Allowed : 0.24 % Favored : 99.73 % 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: -0.87 (0.13), residues: 4254 helix: 1.12 (0.14), residues: 1334 sheet: -0.34 (0.19), residues: 728 loop : -1.82 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 271 HIS 0.006 0.001 HIS F 374 PHE 0.032 0.001 PHE B 906 TYR 0.016 0.001 TYR C1067 ARG 0.004 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 3.981 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.4470 time to fit residues: 104.6562 Evaluate side-chains 93 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 3.761 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 360 optimal weight: 7.9990 chunk 323 optimal weight: 40.0000 chunk 179 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 chunk 172 optimal weight: 6.9990 chunk 334 optimal weight: 50.0000 chunk 129 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 249 optimal weight: 40.0000 chunk 387 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 607 GLN A1036 GLN A1048 HIS ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 544 ASN B 804 GLN C 487 ASN C 901 GLN C 914 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS F 63 ASN F 81 GLN F 98 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 35933 Z= 0.436 Angle : 0.697 11.434 48882 Z= 0.355 Chirality : 0.049 0.589 5645 Planarity : 0.005 0.051 6228 Dihedral : 7.734 59.642 6196 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.97 % Favored : 91.96 % Rotamer: Outliers : 0.42 % Allowed : 8.51 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 4254 helix: 0.96 (0.14), residues: 1381 sheet: -0.52 (0.19), residues: 699 loop : -1.92 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 477 HIS 0.009 0.001 HIS A1048 PHE 0.032 0.002 PHE C1121 TYR 0.037 0.002 TYR C 421 ARG 0.010 0.001 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 4.211 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 110 average time/residue: 0.4479 time to fit residues: 88.7852 Evaluate side-chains 98 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 3.835 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3282 time to fit residues: 10.1429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 215 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 322 optimal weight: 20.0000 chunk 264 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 388 optimal weight: 50.0000 chunk 419 optimal weight: 40.0000 chunk 345 optimal weight: 40.0000 chunk 385 optimal weight: 6.9990 chunk 132 optimal weight: 30.0000 chunk 311 optimal weight: 50.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 919 ASN C 957 GLN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN H 340 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 35933 Z= 0.346 Angle : 0.624 10.331 48882 Z= 0.317 Chirality : 0.047 0.561 5645 Planarity : 0.004 0.051 6228 Dihedral : 7.268 58.764 6196 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.10 % Favored : 92.83 % Rotamer: Outliers : 1.30 % Allowed : 11.79 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 4254 helix: 1.09 (0.14), residues: 1372 sheet: -0.53 (0.19), residues: 698 loop : -1.92 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 271 HIS 0.010 0.001 HIS F 228 PHE 0.027 0.002 PHE C1121 TYR 0.022 0.001 TYR C1067 ARG 0.007 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 94 time to evaluate : 4.127 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 25 residues processed: 139 average time/residue: 0.4259 time to fit residues: 106.0532 Evaluate side-chains 113 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 3.990 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3083 time to fit residues: 20.0173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 383 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 42 optimal weight: 40.0000 chunk 185 optimal weight: 0.9990 chunk 260 optimal weight: 5.9990 chunk 389 optimal weight: 40.0000 chunk 412 optimal weight: 10.0000 chunk 203 optimal weight: 0.7980 chunk 369 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 ASN H 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35933 Z= 0.251 Angle : 0.578 9.653 48882 Z= 0.292 Chirality : 0.045 0.545 5645 Planarity : 0.004 0.050 6228 Dihedral : 6.820 59.283 6196 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.77 % Favored : 93.16 % Rotamer: Outliers : 1.30 % Allowed : 13.86 % Favored : 84.84 % 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: -0.82 (0.13), residues: 4254 helix: 1.25 (0.14), residues: 1372 sheet: -0.35 (0.19), residues: 725 loop : -1.88 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 477 HIS 0.014 0.001 HIS F 228 PHE 0.021 0.001 PHE C1121 TYR 0.018 0.001 TYR C1067 ARG 0.006 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 94 time to evaluate : 3.984 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 28 residues processed: 134 average time/residue: 0.4336 time to fit residues: 104.7453 Evaluate side-chains 116 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 3.742 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3334 time to fit residues: 22.4996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 343 optimal weight: 30.0000 chunk 234 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 307 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 352 optimal weight: 20.0000 chunk 285 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 210 optimal weight: 6.9990 chunk 370 optimal weight: 50.0000 chunk 104 optimal weight: 2.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN C 655 HIS C1005 GLN F 137 ASN F 524 GLN H 96 GLN H 572 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35933 Z= 0.282 Angle : 0.587 9.647 48882 Z= 0.296 Chirality : 0.046 0.533 5645 Planarity : 0.004 0.049 6228 Dihedral : 6.513 58.971 6196 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.84 % Favored : 93.09 % Rotamer: Outliers : 1.46 % Allowed : 15.03 % Favored : 83.51 % 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: -0.80 (0.13), residues: 4254 helix: 1.29 (0.14), residues: 1373 sheet: -0.49 (0.19), residues: 732 loop : -1.83 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 477 HIS 0.012 0.001 HIS F 228 PHE 0.023 0.001 PHE C1121 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 92 time to evaluate : 3.856 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 30 residues processed: 142 average time/residue: 0.4202 time to fit residues: 107.2429 Evaluate side-chains 117 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 87 time to evaluate : 3.875 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3360 time to fit residues: 24.0373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 138 optimal weight: 30.0000 chunk 371 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 242 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 413 optimal weight: 9.9990 chunk 342 optimal weight: 40.0000 chunk 191 optimal weight: 4.9990 chunk 34 optimal weight: 30.0000 chunk 136 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 35933 Z= 0.382 Angle : 0.640 9.877 48882 Z= 0.323 Chirality : 0.047 0.529 5645 Planarity : 0.004 0.048 6228 Dihedral : 6.540 59.996 6196 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.71 % Favored : 92.22 % Rotamer: Outliers : 1.09 % Allowed : 16.33 % Favored : 82.59 % 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: -0.94 (0.13), residues: 4254 helix: 1.16 (0.14), residues: 1372 sheet: -0.58 (0.19), residues: 696 loop : -1.88 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 477 HIS 0.015 0.001 HIS F 228 PHE 0.027 0.002 PHE C1121 TYR 0.022 0.001 TYR A1067 ARG 0.006 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 87 time to evaluate : 3.951 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 25 residues processed: 125 average time/residue: 0.4459 time to fit residues: 100.6148 Evaluate side-chains 111 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 86 time to evaluate : 4.303 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3493 time to fit residues: 21.8231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 398 optimal weight: 30.0000 chunk 46 optimal weight: 30.0000 chunk 235 optimal weight: 40.0000 chunk 301 optimal weight: 0.8980 chunk 233 optimal weight: 10.0000 chunk 347 optimal weight: 50.0000 chunk 230 optimal weight: 0.0370 chunk 411 optimal weight: 50.0000 chunk 257 optimal weight: 7.9990 chunk 250 optimal weight: 9.9990 chunk 190 optimal weight: 0.2980 overall best weight: 3.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN C1011 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 35933 Z= 0.351 Angle : 0.632 10.278 48882 Z= 0.319 Chirality : 0.047 0.511 5645 Planarity : 0.004 0.048 6228 Dihedral : 6.504 59.884 6196 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.38 % Favored : 92.52 % Rotamer: Outliers : 1.14 % Allowed : 17.02 % Favored : 81.84 % 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: -0.92 (0.13), residues: 4254 helix: 1.20 (0.14), residues: 1362 sheet: -0.56 (0.19), residues: 720 loop : -1.89 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 477 HIS 0.015 0.001 HIS F 228 PHE 0.026 0.002 PHE C1121 TYR 0.022 0.001 TYR A1067 ARG 0.006 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 89 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 17 residues processed: 128 average time/residue: 0.4367 time to fit residues: 100.3629 Evaluate side-chains 102 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 4.234 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3420 time to fit residues: 16.7083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 254 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 245 optimal weight: 20.0000 chunk 123 optimal weight: 0.1980 chunk 80 optimal weight: 0.0040 chunk 79 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 203 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 323 optimal weight: 50.0000 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 953 ASN H 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 35933 Z= 0.156 Angle : 0.556 9.733 48882 Z= 0.277 Chirality : 0.044 0.474 5645 Planarity : 0.004 0.049 6228 Dihedral : 5.955 59.729 6196 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.81 % Favored : 94.12 % Rotamer: Outliers : 0.45 % Allowed : 17.28 % Favored : 82.27 % 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: -0.61 (0.13), residues: 4254 helix: 1.50 (0.14), residues: 1362 sheet: -0.35 (0.19), residues: 725 loop : -1.75 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.015 0.001 HIS F 228 PHE 0.012 0.001 PHE B1075 TYR 0.017 0.001 TYR C1067 ARG 0.005 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 3.904 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 107 average time/residue: 0.4438 time to fit residues: 85.1412 Evaluate side-chains 91 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 3.818 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3773 time to fit residues: 9.8179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 374 optimal weight: 6.9990 chunk 394 optimal weight: 30.0000 chunk 359 optimal weight: 6.9990 chunk 383 optimal weight: 8.9990 chunk 230 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 301 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 346 optimal weight: 40.0000 chunk 362 optimal weight: 4.9990 chunk 382 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 824 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 953 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 35933 Z= 0.364 Angle : 0.646 13.408 48882 Z= 0.324 Chirality : 0.047 0.495 5645 Planarity : 0.004 0.048 6228 Dihedral : 6.190 59.008 6196 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.10 % Favored : 92.81 % Rotamer: Outliers : 0.58 % Allowed : 17.78 % Favored : 81.63 % 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: -0.83 (0.13), residues: 4254 helix: 1.30 (0.14), residues: 1368 sheet: -0.60 (0.20), residues: 685 loop : -1.81 (0.13), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1102 HIS 0.014 0.001 HIS F 228 PHE 0.026 0.002 PHE C1121 TYR 0.022 0.001 TYR A1067 ARG 0.007 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 3.837 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 104 average time/residue: 0.4394 time to fit residues: 82.5691 Evaluate side-chains 96 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 3.890 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3369 time to fit residues: 12.3379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 251 optimal weight: 6.9990 chunk 405 optimal weight: 40.0000 chunk 247 optimal weight: 0.1980 chunk 192 optimal weight: 0.6980 chunk 281 optimal weight: 0.8980 chunk 425 optimal weight: 30.0000 chunk 391 optimal weight: 5.9990 chunk 338 optimal weight: 30.0000 chunk 35 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35933 Z= 0.204 Angle : 0.578 11.284 48882 Z= 0.287 Chirality : 0.045 0.472 5645 Planarity : 0.004 0.048 6228 Dihedral : 5.976 59.503 6196 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.21 % Favored : 93.70 % Rotamer: Outliers : 0.16 % Allowed : 18.05 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 4254 helix: 1.46 (0.14), residues: 1365 sheet: -0.36 (0.19), residues: 714 loop : -1.76 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.015 0.001 HIS F 228 PHE 0.017 0.001 PHE C1121 TYR 0.024 0.001 TYR B 200 ARG 0.006 0.000 ARG C 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 3.906 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.4690 time to fit residues: 75.5050 Evaluate side-chains 87 residues out of total 3773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 3.950 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3423 time to fit residues: 7.2606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 269 optimal weight: 0.7980 chunk 360 optimal weight: 20.0000 chunk 103 optimal weight: 40.0000 chunk 312 optimal weight: 30.0000 chunk 50 optimal weight: 0.0980 chunk 94 optimal weight: 1.9990 chunk 339 optimal weight: 30.0000 chunk 141 optimal weight: 10.0000 chunk 348 optimal weight: 50.0000 chunk 42 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.112817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.070264 restraints weight = 166335.397| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 8.26 r_work: 0.2934 rms_B_bonded: 6.43 restraints_weight: 2.0000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2543 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: