Starting phenix.real_space_refine on Thu Apr 11 17:56:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7h_20668/04_2024/6u7h_20668.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7h_20668/04_2024/6u7h_20668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7h_20668/04_2024/6u7h_20668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7h_20668/04_2024/6u7h_20668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7h_20668/04_2024/6u7h_20668.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7h_20668/04_2024/6u7h_20668.pdb" } resolution = 3.1 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= 0.088 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 111 5.16 5 C 14841 2.51 5 N 3741 2.21 5 O 4701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 37": "OE1" <-> "OE2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 453": "OD1" <-> "OD2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 558": "OD1" <-> "OD2" Residue "A TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 607": "OD1" <-> "OD2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 711": "OD1" <-> "OD2" Residue "A ASP 741": "OD1" <-> "OD2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A ARG 776": "NH1" <-> "NH2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A GLU 789": "OE1" <-> "OE2" Residue "A PHE 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 924": "NH1" <-> "NH2" Residue "A GLU 943": "OE1" <-> "OE2" Residue "A GLU 961": "OE1" <-> "OE2" Residue "A ASP 969": "OD1" <-> "OD2" Residue "A GLU 986": "OE1" <-> "OE2" Residue "A TYR 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 999": "OE1" <-> "OE2" Residue "A ASP 1007": "OD1" <-> "OD2" Residue "A GLU 1012": "OE1" <-> "OE2" Residue "A ARG 1023": "NH1" <-> "NH2" Residue "A GLU 1025": "OE1" <-> "OE2" Residue "A TYR 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 124": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B ASP 342": "OD1" <-> "OD2" Residue "B TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 453": "OD1" <-> "OD2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 558": "OD1" <-> "OD2" Residue "B TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 607": "OD1" <-> "OD2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "B PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 711": "OD1" <-> "OD2" Residue "B ASP 741": "OD1" <-> "OD2" Residue "B GLU 743": "OE1" <-> "OE2" Residue "B ARG 744": "NH1" <-> "NH2" Residue "B ARG 776": "NH1" <-> "NH2" Residue "B ASP 785": "OD1" <-> "OD2" Residue "B GLU 789": "OE1" <-> "OE2" Residue "B PHE 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 924": "NH1" <-> "NH2" Residue "B GLU 943": "OE1" <-> "OE2" Residue "B GLU 961": "OE1" <-> "OE2" Residue "B ASP 969": "OD1" <-> "OD2" Residue "B GLU 986": "OE1" <-> "OE2" Residue "B TYR 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 999": "OE1" <-> "OE2" Residue "B ASP 1007": "OD1" <-> "OD2" Residue "B GLU 1012": "OE1" <-> "OE2" Residue "B ARG 1023": "NH1" <-> "NH2" Residue "B GLU 1025": "OE1" <-> "OE2" Residue "B TYR 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C ASP 342": "OD1" <-> "OD2" Residue "C TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 453": "OD1" <-> "OD2" Residue "C PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 558": "OD1" <-> "OD2" Residue "C TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 607": "OD1" <-> "OD2" Residue "C GLU 621": "OE1" <-> "OE2" Residue "C GLU 693": "OE1" <-> "OE2" Residue "C PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 711": "OD1" <-> "OD2" Residue "C ASP 741": "OD1" <-> "OD2" Residue "C GLU 743": "OE1" <-> "OE2" Residue "C ARG 744": "NH1" <-> "NH2" Residue "C ARG 776": "NH1" <-> "NH2" Residue "C ASP 785": "OD1" <-> "OD2" Residue "C GLU 789": "OE1" <-> "OE2" Residue "C PHE 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 924": "NH1" <-> "NH2" Residue "C GLU 943": "OE1" <-> "OE2" Residue "C GLU 961": "OE1" <-> "OE2" Residue "C ASP 969": "OD1" <-> "OD2" Residue "C GLU 986": "OE1" <-> "OE2" Residue "C TYR 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 999": "OE1" <-> "OE2" Residue "C ASP 1007": "OD1" <-> "OD2" Residue "C GLU 1012": "OE1" <-> "OE2" Residue "C ARG 1023": "NH1" <-> "NH2" Residue "C GLU 1025": "OE1" <-> "OE2" Residue "C TYR 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23394 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7438 Classifications: {'peptide': 965} Link IDs: {'PTRANS': 33, 'TRANS': 931} Chain breaks: 3 Chain: "B" Number of atoms: 7438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7438 Classifications: {'peptide': 965} Link IDs: {'PTRANS': 33, 'TRANS': 931} Chain breaks: 3 Chain: "C" Number of atoms: 7438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7438 Classifications: {'peptide': 965} Link IDs: {'PTRANS': 33, 'TRANS': 931} Chain breaks: 3 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 12.19, per 1000 atoms: 0.52 Number of scatterers: 23394 At special positions: 0 Unit cell: (129.32, 134.62, 148.4, 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 111 16.00 O 4701 8.00 N 3741 7.00 C 14841 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 105 " distance=2.04 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 264 " distance=1.99 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 340 " - pdb=" SG CYS A 386 " distance=2.02 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 396 " distance=2.01 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 497 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 556 " distance=2.04 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 630 " distance=2.04 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 619 " distance=2.01 Simple disulfide: pdb=" SG CYS A 715 " - pdb=" SG CYS A 726 " distance=2.03 Simple disulfide: pdb=" SG CYS A 917 " - pdb=" SG CYS A 928 " distance=1.99 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A1014 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 105 " distance=2.04 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=1.99 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 340 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 396 " distance=2.01 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 497 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 630 " distance=2.04 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 619 " distance=2.01 Simple disulfide: pdb=" SG CYS B 715 " - pdb=" SG CYS B 726 " distance=2.03 Simple disulfide: pdb=" SG CYS B 917 " - pdb=" SG CYS B 928 " distance=1.99 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B1014 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 105 " distance=2.04 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 255 " - pdb=" SG CYS C 264 " distance=1.99 Simple disulfide: pdb=" SG CYS C 317 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 340 " - pdb=" SG CYS C 386 " distance=2.02 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 396 " distance=2.01 Simple disulfide: pdb=" SG CYS C 446 " - pdb=" SG CYS C 497 " distance=2.03 Simple disulfide: pdb=" SG CYS C 543 " - pdb=" SG CYS C 556 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 630 " distance=2.04 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 619 " distance=2.01 Simple disulfide: pdb=" SG CYS C 715 " - pdb=" SG CYS C 726 " distance=2.03 Simple disulfide: pdb=" SG CYS C 917 " - pdb=" SG CYS C 928 " distance=1.99 Simple disulfide: pdb=" SG CYS C 967 " - pdb=" SG CYS C1014 " 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 ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN I 4 " - " MAN I 5 " " MAN N 4 " - " MAN N 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " MAN D 6 " - " MAN D 7 " " BMA I 3 " - " MAN I 4 " " MAN I 6 " - " MAN I 7 " " BMA N 3 " - " MAN N 4 " " MAN N 6 " - " MAN N 7 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA I 3 " - " MAN I 6 " " BMA N 3 " - " MAN N 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1210 " - " ASN A 147 " " NAG A1213 " - " ASN A 220 " " NAG A1217 " - " ASN A 326 " " NAG A1218 " - " ASN A 440 " " NAG A1219 " - " ASN A 464 " " NAG A1220 " - " ASN A 518 " " NAG A1223 " - " ASN A 542 " " NAG A1224 " - " ASN A 663 " " NAG A1225 " - " ASN A 671 " " NAG A1226 " - " ASN A 714 " " NAG A1227 " - " ASN A 930 " " NAG B1210 " - " ASN B 147 " " NAG B1213 " - " ASN B 220 " " NAG B1217 " - " ASN B 326 " " NAG B1218 " - " ASN B 440 " " NAG B1219 " - " ASN B 464 " " NAG B1220 " - " ASN B 518 " " NAG B1223 " - " ASN B 542 " " NAG B1224 " - " ASN B 663 " " NAG B1225 " - " ASN B 671 " " NAG B1226 " - " ASN B 714 " " NAG B1227 " - " ASN B 930 " " NAG C1210 " - " ASN C 147 " " NAG C1213 " - " ASN C 220 " " NAG C1217 " - " ASN C 326 " " NAG C1218 " - " ASN C 440 " " NAG C1219 " - " ASN C 464 " " NAG C1220 " - " ASN C 518 " " NAG C1223 " - " ASN C 542 " " NAG C1224 " - " ASN C 663 " " NAG C1225 " - " ASN C 671 " " NAG C1226 " - " ASN C 714 " " NAG C1227 " - " ASN C 930 " " NAG D 1 " - " ASN A 62 " " NAG E 1 " - " ASN A 98 " " NAG F 1 " - " ASN A 171 " " NAG G 1 " - " ASN A 243 " " NAG H 1 " - " ASN A 538 " " NAG I 1 " - " ASN B 62 " " NAG J 1 " - " ASN B 98 " " NAG K 1 " - " ASN B 171 " " NAG L 1 " - " ASN B 243 " " NAG M 1 " - " ASN B 538 " " NAG N 1 " - " ASN C 62 " " NAG O 1 " - " ASN C 98 " " NAG P 1 " - " ASN C 171 " " NAG Q 1 " - " ASN C 243 " " NAG R 1 " - " ASN C 538 " Time building additional restraints: 11.18 Conformation dependent library (CDL) restraints added in 3.8 seconds 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5382 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 36 sheets defined 26.9% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.957A pdb=" N GLY A 523 " --> pdb=" O THR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 628 through 652 Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 663 through 667 Processing helix chain 'A' and resid 671 through 675 removed outlier: 4.262A pdb=" N SER A 674 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 700 removed outlier: 3.564A pdb=" N ILE A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 removed outlier: 4.456A pdb=" N ASN A 714 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 731 removed outlier: 3.551A pdb=" N ASN A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 Processing helix chain 'A' and resid 769 through 779 Processing helix chain 'A' and resid 787 through 811 Processing helix chain 'A' and resid 816 through 851 removed outlier: 4.656A pdb=" N ALA A 822 " --> pdb=" O GLN A 818 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR A 825 " --> pdb=" O GLN A 821 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 870 through 918 removed outlier: 3.880A pdb=" N GLN A 876 " --> pdb=" O PRO A 872 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 880 " --> pdb=" O GLN A 876 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 881 " --> pdb=" O GLN A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1029 Processing helix chain 'B' and resid 257 through 265 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 520 through 524 removed outlier: 3.956A pdb=" N GLY B 523 " --> pdb=" O THR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 614 Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'B' and resid 628 through 652 Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 663 through 667 Processing helix chain 'B' and resid 671 through 675 removed outlier: 4.263A pdb=" N SER B 674 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 700 removed outlier: 3.563A pdb=" N ILE B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 715 removed outlier: 4.455A pdb=" N ASN B 714 " --> pdb=" O ASP B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 731 removed outlier: 3.550A pdb=" N ASN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 755 Processing helix chain 'B' and resid 769 through 779 Processing helix chain 'B' and resid 787 through 811 Processing helix chain 'B' and resid 816 through 851 removed outlier: 4.656A pdb=" N ALA B 822 " --> pdb=" O GLN B 818 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 825 " --> pdb=" O GLN B 821 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 847 " --> pdb=" O SER B 843 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 869 Processing helix chain 'B' and resid 870 through 918 removed outlier: 3.879A pdb=" N GLN B 876 " --> pdb=" O PRO B 872 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 880 " --> pdb=" O GLN B 876 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 881 " --> pdb=" O GLN B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1029 Processing helix chain 'C' and resid 257 through 265 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'C' and resid 520 through 524 removed outlier: 3.956A pdb=" N GLY C 523 " --> pdb=" O THR C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 Processing helix chain 'C' and resid 616 through 624 Processing helix chain 'C' and resid 628 through 652 Processing helix chain 'C' and resid 655 through 662 Processing helix chain 'C' and resid 663 through 667 Processing helix chain 'C' and resid 671 through 675 removed outlier: 4.262A pdb=" N SER C 674 " --> pdb=" O ASN C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 700 removed outlier: 3.564A pdb=" N ILE C 700 " --> pdb=" O LEU C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 715 removed outlier: 4.455A pdb=" N ASN C 714 " --> pdb=" O ASP C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 731 removed outlier: 3.550A pdb=" N ASN C 731 " --> pdb=" O ALA C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 755 Processing helix chain 'C' and resid 769 through 779 Processing helix chain 'C' and resid 787 through 811 Processing helix chain 'C' and resid 816 through 851 removed outlier: 4.657A pdb=" N ALA C 822 " --> pdb=" O GLN C 818 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C 825 " --> pdb=" O GLN C 821 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 847 " --> pdb=" O SER C 843 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU C 851 " --> pdb=" O LEU C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 869 Processing helix chain 'C' and resid 870 through 918 removed outlier: 3.880A pdb=" N GLN C 876 " --> pdb=" O PRO C 872 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C 880 " --> pdb=" O GLN C 876 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 881 " --> pdb=" O GLN C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1029 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.707A pdb=" N THR C 474 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR C 473 " --> pdb=" O LEU C 481 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU C 481 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER C 289 " --> pdb=" O ASN C 450 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 86 removed outlier: 3.721A pdb=" N LEU A 77 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER A 236 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU A 79 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 234 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N CYS A 81 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A 232 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TRP A 83 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE A 230 " --> pdb=" O TRP A 83 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HIS A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N PHE A 201 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 86 removed outlier: 3.721A pdb=" N LEU A 77 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER A 236 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU A 79 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 234 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N CYS A 81 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A 232 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TRP A 83 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE A 230 " --> pdb=" O TRP A 83 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASP A 239 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR A 254 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 241 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE A 252 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN A 243 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 96 removed outlier: 6.751A pdb=" N LYS A 135 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL A 217 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 133 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N PHE A 219 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR A 131 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 140 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 184 " --> pdb=" O CYS A 168 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL A 170 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE A 182 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR A 172 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER A 180 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE A 174 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 278 removed outlier: 3.642A pdb=" N GLY A 512 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.674A pdb=" N SER A 289 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU A 481 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TYR A 473 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR A 472 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 329 removed outlier: 4.397A pdb=" N VAL A 325 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP A 307 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 327 " --> pdb=" O TYR A 305 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR A 305 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU A 329 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 303 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A 384 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY A 422 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 323 through 329 removed outlier: 4.397A pdb=" N VAL A 325 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP A 307 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 327 " --> pdb=" O TYR A 305 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR A 305 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU A 329 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 303 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR A 409 " --> pdb=" O TRP A 404 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TRP A 404 " --> pdb=" O TYR A 409 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N THR A 411 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA A 402 " --> pdb=" O THR A 411 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 546 through 550 Processing sheet with id=AB1, first strand: chain 'A' and resid 583 through 598 removed outlier: 6.511A pdb=" N GLN A 956 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP A 588 " --> pdb=" O PRO A 954 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 590 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU A 952 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL A 592 " --> pdb=" O THR A 950 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR A 950 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A 594 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 948 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TYR A 596 " --> pdb=" O VAL A 946 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 946 " --> pdb=" O TYR A 596 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN A 598 " --> pdb=" O GLY A 944 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY A 944 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 935 " --> pdb=" O THR A 950 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU A 952 " --> pdb=" O HIS A 933 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N HIS A 933 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 604 through 606 Processing sheet with id=AB3, first strand: chain 'A' and resid 1008 through 1011 Processing sheet with id=AB4, first strand: chain 'A' and resid 981 through 986 Processing sheet with id=AB5, first strand: chain 'B' and resid 69 through 86 removed outlier: 3.721A pdb=" N LEU B 77 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER B 236 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU B 79 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU B 234 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N CYS B 81 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL B 232 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP B 83 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE B 230 " --> pdb=" O TRP B 83 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N PHE B 201 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 69 through 86 removed outlier: 3.721A pdb=" N LEU B 77 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER B 236 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU B 79 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU B 234 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N CYS B 81 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL B 232 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP B 83 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE B 230 " --> pdb=" O TRP B 83 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASP B 239 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR B 254 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 241 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN B 243 " --> pdb=" O ALA B 250 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 94 through 96 removed outlier: 6.751A pdb=" N LYS B 135 " --> pdb=" O GLU B 215 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL B 217 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 133 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE B 219 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR B 131 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 140 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 184 " --> pdb=" O CYS B 168 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL B 170 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE B 182 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR B 172 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER B 180 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE B 174 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 274 through 278 removed outlier: 3.643A pdb=" N GLY B 512 " --> pdb=" O VAL B 504 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 288 through 291 removed outlier: 6.674A pdb=" N SER B 289 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU B 481 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR B 473 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR B 472 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 323 through 329 removed outlier: 4.397A pdb=" N VAL B 325 " --> pdb=" O ASP B 307 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP B 307 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE B 327 " --> pdb=" O TYR B 305 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR B 305 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B 329 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL B 303 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER B 384 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY B 422 " --> pdb=" O PHE B 382 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 323 through 329 removed outlier: 4.397A pdb=" N VAL B 325 " --> pdb=" O ASP B 307 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP B 307 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE B 327 " --> pdb=" O TYR B 305 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR B 305 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B 329 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL B 303 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR B 409 " --> pdb=" O TRP B 404 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TRP B 404 " --> pdb=" O TYR B 409 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N THR B 411 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA B 402 " --> pdb=" O THR B 411 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 546 through 550 Processing sheet with id=AC4, first strand: chain 'B' and resid 583 through 598 removed outlier: 6.511A pdb=" N GLN B 956 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP B 588 " --> pdb=" O PRO B 954 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE B 590 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 952 " --> pdb=" O ILE B 590 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B 592 " --> pdb=" O THR B 950 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR B 950 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B 594 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B 948 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYR B 596 " --> pdb=" O VAL B 946 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 946 " --> pdb=" O TYR B 596 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN B 598 " --> pdb=" O GLY B 944 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY B 944 " --> pdb=" O GLN B 598 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 935 " --> pdb=" O THR B 950 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 952 " --> pdb=" O HIS B 933 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N HIS B 933 " --> pdb=" O LEU B 952 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 604 through 606 Processing sheet with id=AC6, first strand: chain 'B' and resid 1008 through 1011 Processing sheet with id=AC7, first strand: chain 'B' and resid 981 through 986 Processing sheet with id=AC8, first strand: chain 'C' and resid 69 through 86 removed outlier: 3.721A pdb=" N LEU C 77 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER C 236 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU C 79 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU C 234 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N CYS C 81 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL C 232 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP C 83 " --> pdb=" O PHE C 230 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE C 230 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE C 201 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 69 through 86 removed outlier: 3.721A pdb=" N LEU C 77 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER C 236 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU C 79 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU C 234 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N CYS C 81 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL C 232 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP C 83 " --> pdb=" O PHE C 230 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE C 230 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASP C 239 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR C 254 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU C 241 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE C 252 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN C 243 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 94 through 96 removed outlier: 6.751A pdb=" N LYS C 135 " --> pdb=" O GLU C 215 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL C 217 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 133 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE C 219 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR C 131 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 140 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 184 " --> pdb=" O CYS C 168 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL C 170 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N PHE C 182 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C 172 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER C 180 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE C 174 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 274 through 278 removed outlier: 3.642A pdb=" N GLY C 512 " --> pdb=" O VAL C 504 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 323 through 329 removed outlier: 4.397A pdb=" N VAL C 325 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP C 307 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE C 327 " --> pdb=" O TYR C 305 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR C 305 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU C 329 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 303 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER C 384 " --> pdb=" O SER C 420 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY C 422 " --> pdb=" O PHE C 382 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 323 through 329 removed outlier: 4.397A pdb=" N VAL C 325 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP C 307 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE C 327 " --> pdb=" O TYR C 305 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR C 305 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU C 329 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 303 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR C 409 " --> pdb=" O TRP C 404 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TRP C 404 " --> pdb=" O TYR C 409 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N THR C 411 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA C 402 " --> pdb=" O THR C 411 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 546 through 550 Processing sheet with id=AD6, first strand: chain 'C' and resid 583 through 598 removed outlier: 6.511A pdb=" N GLN C 956 " --> pdb=" O SER C 586 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP C 588 " --> pdb=" O PRO C 954 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE C 590 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU C 952 " --> pdb=" O ILE C 590 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL C 592 " --> pdb=" O THR C 950 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR C 950 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL C 594 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU C 948 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYR C 596 " --> pdb=" O VAL C 946 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 946 " --> pdb=" O TYR C 596 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN C 598 " --> pdb=" O GLY C 944 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY C 944 " --> pdb=" O GLN C 598 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 935 " --> pdb=" O THR C 950 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C 952 " --> pdb=" O HIS C 933 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N HIS C 933 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 604 through 606 Processing sheet with id=AD8, first strand: chain 'C' and resid 1008 through 1011 Processing sheet with id=AD9, first strand: chain 'C' and resid 981 through 986 1000 hydrogen bonds defined for protein. 2700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.51 Time building geometry restraints manager: 11.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6459 1.33 - 1.45: 4544 1.45 - 1.57: 12715 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 23862 Sorted by residual: bond pdb=" CE1 HIS C 949 " pdb=" NE2 HIS C 949 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.70e+01 bond pdb=" CE1 HIS B 949 " pdb=" NE2 HIS B 949 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.68e+01 bond pdb=" CE1 HIS A 949 " pdb=" NE2 HIS A 949 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.68e+01 bond pdb=" C1 MAN I 5 " pdb=" O5 MAN I 5 " ideal model delta sigma weight residual 1.399 1.475 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C1 MAN N 5 " pdb=" O5 MAN N 5 " ideal model delta sigma weight residual 1.399 1.475 -0.076 2.00e-02 2.50e+03 1.44e+01 ... (remaining 23857 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.89: 501 105.89 - 113.09: 12359 113.09 - 120.29: 10661 120.29 - 127.48: 8852 127.48 - 134.68: 132 Bond angle restraints: 32505 Sorted by residual: angle pdb=" CA ASP A 635 " pdb=" CB ASP A 635 " pdb=" CG ASP A 635 " ideal model delta sigma weight residual 112.60 118.90 -6.30 1.00e+00 1.00e+00 3.98e+01 angle pdb=" CA ASP B 635 " pdb=" CB ASP B 635 " pdb=" CG ASP B 635 " ideal model delta sigma weight residual 112.60 118.89 -6.29 1.00e+00 1.00e+00 3.95e+01 angle pdb=" CA ASP C 635 " pdb=" CB ASP C 635 " pdb=" CG ASP C 635 " ideal model delta sigma weight residual 112.60 118.88 -6.28 1.00e+00 1.00e+00 3.94e+01 angle pdb=" CA ASP A 68 " pdb=" CB ASP A 68 " pdb=" CG ASP A 68 " ideal model delta sigma weight residual 112.60 118.83 -6.23 1.00e+00 1.00e+00 3.88e+01 angle pdb=" CA ASP B 68 " pdb=" CB ASP B 68 " pdb=" CG ASP B 68 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.00e+00 1.00e+00 3.87e+01 ... (remaining 32500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.50: 14318 22.50 - 44.99: 634 44.99 - 67.49: 69 67.49 - 89.98: 84 89.98 - 112.48: 36 Dihedral angle restraints: 15141 sinusoidal: 6729 harmonic: 8412 Sorted by residual: dihedral pdb=" CA GLY B 539 " pdb=" C GLY B 539 " pdb=" N THR B 540 " pdb=" CA THR B 540 " ideal model delta harmonic sigma weight residual 180.00 150.71 29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA GLY A 539 " pdb=" C GLY A 539 " pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA GLY C 539 " pdb=" C GLY C 539 " pdb=" N THR C 540 " pdb=" CA THR C 540 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 15138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2688 0.105 - 0.211: 1168 0.211 - 0.316: 125 0.316 - 0.421: 27 0.421 - 0.527: 18 Chirality restraints: 4026 Sorted by residual: chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.38e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.32e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.29e+01 ... (remaining 4023 not shown) Planarity restraints: 4089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1223 " 0.238 2.00e-02 2.50e+03 1.98e-01 4.89e+02 pdb=" C7 NAG B1223 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG B1223 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG B1223 " -0.327 2.00e-02 2.50e+03 pdb=" O7 NAG B1223 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1223 " -0.238 2.00e-02 2.50e+03 1.98e-01 4.88e+02 pdb=" C7 NAG C1223 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG C1223 " -0.167 2.00e-02 2.50e+03 pdb=" N2 NAG C1223 " 0.327 2.00e-02 2.50e+03 pdb=" O7 NAG C1223 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1223 " 0.238 2.00e-02 2.50e+03 1.98e-01 4.88e+02 pdb=" C7 NAG A1223 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG A1223 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG A1223 " -0.327 2.00e-02 2.50e+03 pdb=" O7 NAG A1223 " -0.015 2.00e-02 2.50e+03 ... (remaining 4086 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4597 2.81 - 3.33: 23641 3.33 - 3.85: 38048 3.85 - 4.38: 45244 4.38 - 4.90: 76650 Nonbonded interactions: 188180 Sorted by model distance: nonbonded pdb=" OG SER A 665 " pdb=" O6 NAG A1224 " model vdw 2.282 2.440 nonbonded pdb=" OG SER B 665 " pdb=" O6 NAG B1224 " model vdw 2.282 2.440 nonbonded pdb=" OG SER C 665 " pdb=" O6 NAG C1224 " model vdw 2.283 2.440 nonbonded pdb=" O4 NAG B1210 " pdb=" O6 NAG B1210 " model vdw 2.317 2.440 nonbonded pdb=" O4 NAG A1210 " pdb=" O6 NAG A1210 " model vdw 2.317 2.440 ... (remaining 188175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'Q' } 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: 0.990 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: 0.030 Extract box with map and model: 5.970 Check model and map are aligned: 0.330 Set scattering table: 0.220 Process input model: 64.070 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.013 0.076 23862 Z= 0.866 Angle : 1.782 8.991 32505 Z= 1.170 Chirality : 0.112 0.527 4026 Planarity : 0.014 0.198 4041 Dihedral : 15.362 112.478 9642 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.24 % Allowed : 2.28 % Favored : 97.48 % Cbeta Deviations : 1.23 % 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 (0.14), residues: 2871 helix: -0.46 (0.18), residues: 657 sheet: 0.76 (0.20), residues: 564 loop : -1.21 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.011 TRP A 588 HIS 0.015 0.005 HIS A 846 PHE 0.080 0.013 PHE A 809 TYR 0.098 0.016 TYR A 237 ARG 0.040 0.006 ARG B 261 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 244 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 802 MET cc_start: 0.9242 (mmm) cc_final: 0.8827 (tpp) REVERT: A 943 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 997 MET cc_start: 0.8312 (mmt) cc_final: 0.7997 (mpp) REVERT: B 644 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7998 (mm-30) REVERT: B 943 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7780 (mt-10) REVERT: C 300 MET cc_start: 0.8797 (ttm) cc_final: 0.8418 (ttm) REVERT: C 890 ASN cc_start: 0.8691 (m-40) cc_final: 0.8455 (m110) outliers start: 6 outliers final: 3 residues processed: 250 average time/residue: 0.3379 time to fit residues: 136.3500 Evaluate side-chains 142 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 1019 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS A 266 GLN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN A 731 ASN A 824 GLN A 831 ASN A 850 GLN A 933 HIS B 200 HIS ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN B 731 ASN B 824 GLN B 831 ASN B 850 GLN B 933 HIS C 200 HIS C 365 ASN C 731 ASN C 824 GLN C 831 ASN C 850 GLN C 933 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23862 Z= 0.242 Angle : 0.681 6.837 32505 Z= 0.372 Chirality : 0.049 0.247 4026 Planarity : 0.004 0.035 4041 Dihedral : 11.192 75.374 4794 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.56 % Allowed : 4.69 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 2871 helix: 1.20 (0.20), residues: 663 sheet: 0.90 (0.19), residues: 633 loop : -0.78 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 588 HIS 0.003 0.001 HIS C 345 PHE 0.022 0.002 PHE C 379 TYR 0.023 0.002 TYR A 957 ARG 0.005 0.001 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 161 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 943 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7856 (mt-10) REVERT: A 997 MET cc_start: 0.8253 (mmt) cc_final: 0.7879 (mmm) REVERT: B 997 MET cc_start: 0.8038 (mpp) cc_final: 0.7565 (mmm) REVERT: C 300 MET cc_start: 0.8511 (ttm) cc_final: 0.8270 (ttm) REVERT: C 997 MET cc_start: 0.8036 (mpp) cc_final: 0.7390 (mpp) outliers start: 39 outliers final: 19 residues processed: 193 average time/residue: 0.3084 time to fit residues: 100.8343 Evaluate side-chains 132 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 831 ASN Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 831 ASN Chi-restraints excluded: chain C residue 1019 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 262 optimal weight: 5.9990 chunk 283 optimal weight: 30.0000 chunk 233 optimal weight: 6.9990 chunk 259 optimal weight: 4.9990 chunk 89 optimal weight: 50.0000 chunk 210 optimal weight: 8.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN B 831 ASN B1020 ASN C 831 ASN C1020 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23862 Z= 0.322 Angle : 0.624 7.563 32505 Z= 0.332 Chirality : 0.047 0.231 4026 Planarity : 0.004 0.036 4041 Dihedral : 9.193 63.356 4794 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.28 % Allowed : 6.13 % Favored : 92.59 % 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: 0.23 (0.16), residues: 2871 helix: 1.60 (0.20), residues: 654 sheet: 0.63 (0.19), residues: 669 loop : -0.70 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 963 HIS 0.005 0.001 HIS B 846 PHE 0.017 0.002 PHE B 230 TYR 0.020 0.001 TYR B 957 ARG 0.004 0.000 ARG B 685 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 2.551 Fit side-chains revert: symmetry clash REVERT: A 802 MET cc_start: 0.9312 (tpp) cc_final: 0.9053 (tpp) REVERT: A 943 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7876 (mt-10) REVERT: A 997 MET cc_start: 0.8116 (mmt) cc_final: 0.7820 (mmm) REVERT: A 1005 MET cc_start: 0.3568 (mmm) cc_final: 0.3352 (mmm) REVERT: B 423 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8549 (p0) REVERT: B 425 ILE cc_start: 0.9231 (mm) cc_final: 0.8997 (mt) REVERT: B 832 LYS cc_start: 0.9196 (ttmm) cc_final: 0.8938 (ttpp) REVERT: B 997 MET cc_start: 0.7771 (mpp) cc_final: 0.7538 (mmm) REVERT: C 300 MET cc_start: 0.8497 (ttm) cc_final: 0.8134 (ttm) REVERT: C 802 MET cc_start: 0.9254 (mmm) cc_final: 0.8891 (tpp) REVERT: C 997 MET cc_start: 0.7822 (mpp) cc_final: 0.7594 (mmm) outliers start: 32 outliers final: 16 residues processed: 148 average time/residue: 0.3266 time to fit residues: 81.0213 Evaluate side-chains 126 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 912 GLN Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 1019 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 chunk 262 optimal weight: 6.9990 chunk 278 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 GLN A 831 ASN B 831 ASN C 256 ASN C 831 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23862 Z= 0.240 Angle : 0.567 7.817 32505 Z= 0.302 Chirality : 0.046 0.243 4026 Planarity : 0.004 0.038 4041 Dihedral : 7.645 55.320 4794 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.44 % Allowed : 7.13 % Favored : 91.43 % 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: 0.36 (0.16), residues: 2871 helix: 2.09 (0.21), residues: 645 sheet: 0.48 (0.19), residues: 693 loop : -0.68 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 419 HIS 0.004 0.001 HIS B 846 PHE 0.014 0.001 PHE A 382 TYR 0.017 0.001 TYR B 957 ARG 0.009 0.000 ARG A 685 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 122 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 943 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7865 (mt-10) REVERT: A 997 MET cc_start: 0.8196 (mmt) cc_final: 0.7927 (mmm) REVERT: A 1005 MET cc_start: 0.3899 (mmm) cc_final: 0.3663 (mmm) REVERT: B 423 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8354 (p0) REVERT: B 709 ASP cc_start: 0.8146 (p0) cc_final: 0.7909 (p0) REVERT: B 997 MET cc_start: 0.7838 (mpp) cc_final: 0.7593 (mmm) REVERT: B 1005 MET cc_start: 0.3652 (mmm) cc_final: 0.3444 (mmm) REVERT: C 300 MET cc_start: 0.8481 (ttm) cc_final: 0.8277 (ttm) REVERT: C 709 ASP cc_start: 0.8352 (p0) cc_final: 0.8121 (p0) REVERT: C 802 MET cc_start: 0.9252 (mmm) cc_final: 0.8918 (tpp) REVERT: C 997 MET cc_start: 0.7808 (mpp) cc_final: 0.7586 (mmm) outliers start: 36 outliers final: 24 residues processed: 150 average time/residue: 0.3220 time to fit residues: 81.5693 Evaluate side-chains 132 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 912 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 831 ASN Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 831 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 207 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 237 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 256 ASN A 831 ASN B 80 ASN B 256 ASN B 502 GLN B 824 GLN B 831 ASN ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C 831 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23862 Z= 0.228 Angle : 0.549 10.776 32505 Z= 0.292 Chirality : 0.045 0.220 4026 Planarity : 0.003 0.036 4041 Dihedral : 7.053 53.072 4791 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.36 % Allowed : 8.05 % Favored : 90.58 % 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: 0.38 (0.16), residues: 2871 helix: 2.15 (0.21), residues: 645 sheet: 0.50 (0.19), residues: 687 loop : -0.70 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 419 HIS 0.004 0.001 HIS B 846 PHE 0.014 0.001 PHE A 798 TYR 0.022 0.001 TYR A 990 ARG 0.004 0.000 ARG B 685 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 119 time to evaluate : 2.737 Fit side-chains revert: symmetry clash REVERT: A 943 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7887 (mt-10) REVERT: A 997 MET cc_start: 0.8181 (mmt) cc_final: 0.7925 (mmm) REVERT: A 1005 MET cc_start: 0.3968 (mmm) cc_final: 0.3761 (mmm) REVERT: B 423 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8327 (p0) REVERT: B 709 ASP cc_start: 0.8177 (p0) cc_final: 0.7927 (p0) REVERT: B 997 MET cc_start: 0.7834 (mpp) cc_final: 0.7619 (mmm) REVERT: B 1005 MET cc_start: 0.3583 (mmm) cc_final: 0.3365 (mmm) REVERT: C 300 MET cc_start: 0.8480 (ttm) cc_final: 0.8220 (ttm) REVERT: C 709 ASP cc_start: 0.8358 (p0) cc_final: 0.8098 (p0) outliers start: 34 outliers final: 25 residues processed: 145 average time/residue: 0.3098 time to fit residues: 77.6896 Evaluate side-chains 137 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 912 GLN Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 805 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 278 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 92 optimal weight: 0.0870 chunk 146 optimal weight: 7.9990 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 ASN ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN B 949 HIS C 80 ASN ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 HIS ** C 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23862 Z= 0.284 Angle : 0.557 10.042 32505 Z= 0.295 Chirality : 0.045 0.214 4026 Planarity : 0.004 0.041 4041 Dihedral : 6.620 52.694 4791 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.68 % Allowed : 8.33 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2871 helix: 2.29 (0.21), residues: 645 sheet: 0.43 (0.19), residues: 717 loop : -0.66 (0.17), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 419 HIS 0.008 0.002 HIS B 297 PHE 0.016 0.001 PHE C 769 TYR 0.020 0.001 TYR B 550 ARG 0.003 0.000 ARG B 744 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 111 time to evaluate : 2.610 Fit side-chains revert: symmetry clash REVERT: A 943 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7929 (mt-10) REVERT: A 997 MET cc_start: 0.8128 (mmt) cc_final: 0.7827 (mmm) REVERT: B 177 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7654 (pm20) REVERT: B 423 ASP cc_start: 0.8468 (p0) cc_final: 0.8236 (p0) REVERT: B 709 ASP cc_start: 0.8200 (p0) cc_final: 0.7995 (p0) REVERT: B 997 MET cc_start: 0.7786 (mpp) cc_final: 0.7546 (mmm) REVERT: B 1005 MET cc_start: 0.3675 (mmm) cc_final: 0.3469 (mmm) REVERT: C 300 MET cc_start: 0.8516 (ttm) cc_final: 0.8290 (ttm) REVERT: C 709 ASP cc_start: 0.8346 (p0) cc_final: 0.8095 (p0) REVERT: C 802 MET cc_start: 0.9243 (mmm) cc_final: 0.8924 (tpp) outliers start: 42 outliers final: 27 residues processed: 144 average time/residue: 0.2987 time to fit residues: 76.1808 Evaluate side-chains 134 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 912 GLN Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 805 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 ASN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 ASN ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 ASN ** C 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23862 Z= 0.243 Angle : 0.534 7.027 32505 Z= 0.285 Chirality : 0.045 0.217 4026 Planarity : 0.003 0.046 4041 Dihedral : 6.407 52.849 4791 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.40 % Allowed : 8.65 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.16), residues: 2871 helix: 2.33 (0.21), residues: 645 sheet: 0.43 (0.19), residues: 687 loop : -0.70 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 419 HIS 0.004 0.001 HIS B 345 PHE 0.014 0.001 PHE C 229 TYR 0.015 0.001 TYR A 550 ARG 0.010 0.000 ARG C 685 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 111 time to evaluate : 2.911 Fit side-chains revert: symmetry clash REVERT: A 943 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7920 (mt-10) REVERT: A 997 MET cc_start: 0.8152 (mmt) cc_final: 0.7816 (mmm) REVERT: B 177 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: B 423 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8172 (p0) REVERT: B 709 ASP cc_start: 0.8194 (p0) cc_final: 0.7977 (p0) REVERT: B 997 MET cc_start: 0.7798 (mpp) cc_final: 0.7560 (mmm) REVERT: B 1005 MET cc_start: 0.3595 (mmm) cc_final: 0.3376 (mmm) REVERT: C 300 MET cc_start: 0.8512 (ttm) cc_final: 0.8284 (ttm) REVERT: C 709 ASP cc_start: 0.8353 (p0) cc_final: 0.8092 (p0) outliers start: 35 outliers final: 28 residues processed: 136 average time/residue: 0.3114 time to fit residues: 73.6858 Evaluate side-chains 138 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 912 GLN Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 831 ASN Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 831 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 189 optimal weight: 30.0000 chunk 137 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 218 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 ASN ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 ASN ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 ASN ** C 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23862 Z= 0.294 Angle : 0.549 8.013 32505 Z= 0.292 Chirality : 0.045 0.215 4026 Planarity : 0.004 0.055 4041 Dihedral : 6.313 52.833 4791 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.60 % Allowed : 8.69 % Favored : 89.70 % 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: 0.33 (0.16), residues: 2871 helix: 2.26 (0.21), residues: 648 sheet: 0.39 (0.19), residues: 666 loop : -0.75 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 419 HIS 0.005 0.001 HIS A 846 PHE 0.032 0.001 PHE B 798 TYR 0.016 0.001 TYR A 550 ARG 0.005 0.000 ARG C 689 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 109 time to evaluate : 2.500 Fit side-chains revert: symmetry clash REVERT: A 368 ASN cc_start: 0.9282 (p0) cc_final: 0.8904 (p0) REVERT: A 943 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7924 (mt-10) REVERT: A 997 MET cc_start: 0.8167 (mmt) cc_final: 0.7837 (mmm) REVERT: B 177 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7695 (pm20) REVERT: B 709 ASP cc_start: 0.8196 (p0) cc_final: 0.7951 (p0) REVERT: B 798 PHE cc_start: 0.9118 (t80) cc_final: 0.8842 (t80) REVERT: B 832 LYS cc_start: 0.9271 (ttpt) cc_final: 0.9005 (ttpp) REVERT: B 997 MET cc_start: 0.7862 (mpp) cc_final: 0.7629 (mmm) REVERT: B 1005 MET cc_start: 0.3494 (mmm) cc_final: 0.3276 (mmm) REVERT: C 300 MET cc_start: 0.8489 (ttm) cc_final: 0.8255 (ttm) REVERT: C 709 ASP cc_start: 0.8374 (p0) cc_final: 0.8105 (p0) REVERT: C 802 MET cc_start: 0.9281 (mmm) cc_final: 0.8890 (tpp) outliers start: 40 outliers final: 30 residues processed: 139 average time/residue: 0.3050 time to fit residues: 74.4627 Evaluate side-chains 136 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 912 GLN Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 831 ASN Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 831 ASN Chi-restraints excluded: chain C residue 912 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 242 optimal weight: 8.9990 chunk 258 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 233 optimal weight: 0.2980 chunk 244 optimal weight: 20.0000 chunk 257 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 430 GLN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN ** A 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23862 Z= 0.221 Angle : 0.529 6.984 32505 Z= 0.283 Chirality : 0.044 0.213 4026 Planarity : 0.003 0.055 4041 Dihedral : 6.137 53.955 4791 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.36 % Allowed : 8.85 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2871 helix: 2.26 (0.21), residues: 648 sheet: 0.45 (0.19), residues: 702 loop : -0.74 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 419 HIS 0.020 0.002 HIS B 297 PHE 0.027 0.001 PHE B 798 TYR 0.014 0.001 TYR A 550 ARG 0.001 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 113 time to evaluate : 2.625 Fit side-chains revert: symmetry clash REVERT: A 368 ASN cc_start: 0.9237 (p0) cc_final: 0.8889 (p0) REVERT: A 423 ASP cc_start: 0.8541 (m-30) cc_final: 0.8256 (m-30) REVERT: A 943 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7917 (mt-10) REVERT: A 997 MET cc_start: 0.8178 (mmt) cc_final: 0.7854 (mmm) REVERT: B 177 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7746 (pm20) REVERT: B 635 ASP cc_start: 0.7926 (p0) cc_final: 0.7606 (p0) REVERT: B 709 ASP cc_start: 0.8180 (p0) cc_final: 0.7925 (p0) REVERT: B 798 PHE cc_start: 0.9136 (t80) cc_final: 0.8851 (t80) REVERT: B 832 LYS cc_start: 0.9264 (ttpt) cc_final: 0.8968 (ttpp) REVERT: B 997 MET cc_start: 0.7764 (mpp) cc_final: 0.7519 (mmm) REVERT: B 1005 MET cc_start: 0.3410 (mmm) cc_final: 0.3194 (mmm) REVERT: C 300 MET cc_start: 0.8439 (ttm) cc_final: 0.8205 (ttm) REVERT: C 709 ASP cc_start: 0.8358 (p0) cc_final: 0.8073 (p0) REVERT: C 802 MET cc_start: 0.9266 (mmm) cc_final: 0.8882 (tpp) outliers start: 34 outliers final: 29 residues processed: 136 average time/residue: 0.3115 time to fit residues: 74.0090 Evaluate side-chains 140 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 912 GLN Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 912 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.9980 chunk 273 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 190 optimal weight: 50.0000 chunk 286 optimal weight: 9.9990 chunk 264 optimal weight: 8.9990 chunk 228 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 176 optimal weight: 0.6980 chunk 140 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 GLN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23862 Z= 0.147 Angle : 0.514 15.322 32505 Z= 0.273 Chirality : 0.044 0.214 4026 Planarity : 0.003 0.054 4041 Dihedral : 5.842 57.522 4791 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.92 % Allowed : 9.50 % Favored : 89.58 % 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: 0.46 (0.16), residues: 2871 helix: 2.29 (0.21), residues: 648 sheet: 0.49 (0.18), residues: 708 loop : -0.67 (0.17), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 588 HIS 0.010 0.001 HIS B 297 PHE 0.024 0.001 PHE B 798 TYR 0.012 0.001 TYR C 957 ARG 0.002 0.000 ARG A 642 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 2.395 Fit side-chains revert: symmetry clash REVERT: A 368 ASN cc_start: 0.9192 (p0) cc_final: 0.8847 (p0) REVERT: A 423 ASP cc_start: 0.8530 (m-30) cc_final: 0.8203 (m-30) REVERT: A 943 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7891 (mt-10) REVERT: A 997 MET cc_start: 0.8123 (mmt) cc_final: 0.7794 (mmm) REVERT: B 177 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: B 635 ASP cc_start: 0.7806 (p0) cc_final: 0.7488 (p0) REVERT: B 709 ASP cc_start: 0.8163 (p0) cc_final: 0.7882 (p0) REVERT: B 997 MET cc_start: 0.7734 (mpp) cc_final: 0.7492 (mmm) REVERT: B 1005 MET cc_start: 0.3422 (mmm) cc_final: 0.3209 (mmm) REVERT: C 300 MET cc_start: 0.8482 (ttm) cc_final: 0.8248 (ttm) REVERT: C 709 ASP cc_start: 0.8350 (p0) cc_final: 0.8049 (p0) outliers start: 23 outliers final: 17 residues processed: 138 average time/residue: 0.3025 time to fit residues: 71.9530 Evaluate side-chains 126 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 912 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 69 optimal weight: 0.0060 chunk 210 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN ** A 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 846 HIS C 850 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.096261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.061394 restraints weight = 61049.325| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 4.01 r_work: 0.2727 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23862 Z= 0.255 Angle : 0.539 13.918 32505 Z= 0.285 Chirality : 0.044 0.238 4026 Planarity : 0.004 0.051 4041 Dihedral : 5.887 58.783 4791 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.04 % Allowed : 9.66 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2871 helix: 2.13 (0.21), residues: 666 sheet: 0.46 (0.18), residues: 708 loop : -0.65 (0.17), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 419 HIS 0.007 0.001 HIS A 846 PHE 0.071 0.001 PHE B 769 TYR 0.014 0.001 TYR A 296 ARG 0.001 0.000 ARG B 776 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4113.89 seconds wall clock time: 77 minutes 22.32 seconds (4642.32 seconds total)