Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 16:07:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7h_20668/04_2023/6u7h_20668.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7h_20668/04_2023/6u7h_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_2023/6u7h_20668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7h_20668/04_2023/6u7h_20668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7h_20668/04_2023/6u7h_20668.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7h_20668/04_2023/6u7h_20668.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 11 Time building chain proxies: 12.05, 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: 10.57 Conformation dependent library (CDL) restraints added in 3.5 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: 1.67 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: 9.62 Time building geometry restraints manager: 10.85 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 - 17.43: 12373 17.43 - 34.86: 902 34.86 - 52.29: 141 52.29 - 69.72: 24 69.72 - 87.15: 36 Dihedral angle restraints: 13476 sinusoidal: 5064 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 13473 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.720 Check model and map are aligned: 0.360 Set scattering table: 0.190 Process input model: 61.120 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.240 ------------------------------------------------------------------------------- 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 : 13.268 87.151 7977 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 % 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 *********************** 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 : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 250 average time/residue: 0.3395 time to fit residues: 137.4895 Evaluate side-chains 141 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 138 time to evaluate : 2.582 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2124 time to fit residues: 4.7178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 137 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.8422 moved from start: 0.1816 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= 0.234 Angle : 0.667 7.698 32505 Z= 0.366 Chirality : 0.048 0.247 4026 Planarity : 0.004 0.036 4041 Dihedral : 6.845 24.743 3126 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 2871 helix: 1.21 (0.20), residues: 663 sheet: 0.91 (0.19), residues: 675 loop : -0.77 (0.16), residues: 1533 *********************** 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 191 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 2.512 Fit side-chains outliers start: 33 outliers final: 14 residues processed: 186 average time/residue: 0.3305 time to fit residues: 104.9014 Evaluate side-chains 123 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 2.627 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2239 time to fit residues: 9.7233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 262 optimal weight: 5.9990 chunk 283 optimal weight: 30.0000 chunk 233 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 89 optimal weight: 0.0770 chunk 210 optimal weight: 2.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- 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** B1020 ASN C1020 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 23862 Z= 0.263 Angle : 0.594 6.889 32505 Z= 0.322 Chirality : 0.046 0.230 4026 Planarity : 0.004 0.036 4041 Dihedral : 5.939 23.779 3126 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.76 % 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: 0.37 (0.16), residues: 2871 helix: 1.79 (0.21), residues: 654 sheet: 0.69 (0.18), residues: 714 loop : -0.68 (0.17), residues: 1503 *********************** 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 140 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 2.498 Fit side-chains outliers start: 19 outliers final: 4 residues processed: 137 average time/residue: 0.3125 time to fit residues: 72.1223 Evaluate side-chains 110 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 2.414 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2230 time to fit residues: 4.9296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 175 optimal weight: 0.8980 chunk 262 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 GLN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 23862 Z= 0.270 Angle : 0.568 11.291 32505 Z= 0.305 Chirality : 0.045 0.221 4026 Planarity : 0.004 0.037 4041 Dihedral : 5.501 21.620 3126 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 2871 helix: 2.08 (0.21), residues: 648 sheet: 0.48 (0.19), residues: 693 loop : -0.67 (0.16), residues: 1530 *********************** 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 148 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 2.668 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 142 average time/residue: 0.3177 time to fit residues: 76.5688 Evaluate side-chains 117 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 2.597 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2098 time to fit residues: 8.7666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 0.5980 chunk 158 optimal weight: 0.0020 chunk 4 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 237 optimal weight: 0.8980 chunk 192 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 249 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 824 GLN B 845 ASN B 949 HIS C 824 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 23862 Z= 0.150 Angle : 0.532 11.434 32505 Z= 0.285 Chirality : 0.044 0.219 4026 Planarity : 0.003 0.037 4041 Dihedral : 5.132 21.240 3126 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.36 % 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: 2.27 (0.21), residues: 645 sheet: 0.53 (0.19), residues: 687 loop : -0.69 (0.16), residues: 1539 *********************** 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 138 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 2.748 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 135 average time/residue: 0.3127 time to fit residues: 72.4244 Evaluate side-chains 117 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 2.559 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2387 time to fit residues: 4.3934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 9.9990 chunk 250 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 278 optimal weight: 5.9990 chunk 231 optimal weight: 0.4980 chunk 129 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 23862 Z= 0.211 Angle : 0.523 8.073 32505 Z= 0.281 Chirality : 0.044 0.225 4026 Planarity : 0.003 0.035 4041 Dihedral : 4.962 23.956 3126 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.48 % 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: 0.42 (0.16), residues: 2871 helix: 2.25 (0.21), residues: 645 sheet: 0.50 (0.19), residues: 687 loop : -0.69 (0.16), residues: 1539 *********************** 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 129 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 2.804 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 125 average time/residue: 0.3145 time to fit residues: 67.8672 Evaluate side-chains 116 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 2.713 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2309 time to fit residues: 4.9460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 277 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 overall best weight: 2.5584 ------------------------------------------------------------------------------- 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 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN B 256 ASN B 853 GLN C 949 HIS ** C 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 23862 Z= 0.302 Angle : 0.554 12.079 32505 Z= 0.294 Chirality : 0.044 0.218 4026 Planarity : 0.004 0.038 4041 Dihedral : 4.937 23.294 3126 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.36 % 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: 0.37 (0.16), residues: 2871 helix: 2.21 (0.21), residues: 648 sheet: 0.44 (0.19), residues: 687 loop : -0.71 (0.16), residues: 1536 *********************** 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 120 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 2.488 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 117 average time/residue: 0.3256 time to fit residues: 66.0136 Evaluate side-chains 112 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 2.803 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2322 time to fit residues: 5.9175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 189 optimal weight: 0.0470 chunk 137 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 218 optimal weight: 0.0870 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 GLN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN B 502 GLN ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 23862 Z= 0.134 Angle : 0.505 7.190 32505 Z= 0.272 Chirality : 0.043 0.216 4026 Planarity : 0.004 0.047 4041 Dihedral : 4.740 25.522 3126 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.24 % 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: 2.17 (0.21), residues: 654 sheet: 0.52 (0.18), residues: 708 loop : -0.71 (0.16), residues: 1509 *********************** 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 130 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 128 average time/residue: 0.3272 time to fit residues: 71.8700 Evaluate side-chains 109 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 2.752 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2377 time to fit residues: 4.6795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 242 optimal weight: 9.9990 chunk 258 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 233 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 257 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 824 GLN ** A 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 GLN ** C 790 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: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 23862 Z= 0.162 Angle : 0.498 9.277 32505 Z= 0.267 Chirality : 0.043 0.209 4026 Planarity : 0.003 0.042 4041 Dihedral : 4.620 26.633 3126 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2871 helix: 2.13 (0.21), residues: 666 sheet: 0.55 (0.19), residues: 699 loop : -0.65 (0.16), residues: 1506 *********************** 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 116 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 113 average time/residue: 0.3095 time to fit residues: 61.3452 Evaluate side-chains 108 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 2.558 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2301 time to fit residues: 4.1687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.8980 chunk 273 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 190 optimal weight: 30.0000 chunk 286 optimal weight: 0.9990 chunk 264 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 176 optimal weight: 0.0980 chunk 140 optimal weight: 0.0970 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 23862 Z= 0.137 Angle : 0.493 8.257 32505 Z= 0.264 Chirality : 0.043 0.209 4026 Planarity : 0.004 0.042 4041 Dihedral : 4.542 29.531 3126 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2871 helix: 2.10 (0.21), residues: 672 sheet: 0.60 (0.19), residues: 696 loop : -0.63 (0.16), residues: 1503 ********************** 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 122 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 0.3134 time to fit residues: 65.8357 Evaluate side-chains 110 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 2.518 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2543 time to fit residues: 3.9120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 210 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 228 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 234 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.097589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.062430 restraints weight = 61260.374| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 4.08 r_work: 0.2758 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 23862 Z= 0.187 Angle : 0.500 8.674 32505 Z= 0.266 Chirality : 0.043 0.206 4026 Planarity : 0.004 0.043 4041 Dihedral : 4.508 25.582 3126 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.16 % 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: 0.49 (0.16), residues: 2871 helix: 2.21 (0.21), residues: 666 sheet: 0.49 (0.19), residues: 675 loop : -0.60 (0.16), residues: 1530 =============================================================================== Job complete usr+sys time: 3741.54 seconds wall clock time: 70 minutes 22.49 seconds (4222.49 seconds total)