Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 20:28:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y38_33591/10_2023/7y38_33591_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y38_33591/10_2023/7y38_33591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y38_33591/10_2023/7y38_33591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y38_33591/10_2023/7y38_33591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y38_33591/10_2023/7y38_33591_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y38_33591/10_2023/7y38_33591_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 P 75 5.49 5 S 397 5.16 5 C 33324 2.51 5 N 9266 2.21 5 O 10061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 11": "OD1" <-> "OD2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B ASP 277": "OD1" <-> "OD2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 354": "OD1" <-> "OD2" Residue "B PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 404": "OD1" <-> "OD2" Residue "D ASP 11": "OD1" <-> "OD2" Residue "D ASP 277": "OD1" <-> "OD2" Residue "D ASP 340": "OD1" <-> "OD2" Residue "E ASP 277": "OD1" <-> "OD2" Residue "E TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 234": "OE1" <-> "OE2" Residue "F ASP 322": "OD1" <-> "OD2" Residue "F ASP 354": "OD1" <-> "OD2" Residue "G ASP 9": "OD1" <-> "OD2" Residue "G PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 277": "OD1" <-> "OD2" Residue "H ASP 436": "OD1" <-> "OD2" Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 277": "OD1" <-> "OD2" Residue "I ASP 322": "OD1" <-> "OD2" Residue "I ASP 340": "OD1" <-> "OD2" Residue "K TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 277": "OD1" <-> "OD2" Residue "K TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 42": "OE1" <-> "OE2" Residue "X PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 466": "OD1" <-> "OD2" Residue "X PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 552": "OD1" <-> "OD2" Residue "Y GLU 121": "OE1" <-> "OE2" Residue "Y PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 399": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 53135 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3677 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 471, 3671 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 471, 3671 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3743 Chain: "B" Number of atoms: 3673 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3739 Chain: "C" Number of atoms: 3673 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3739 Chain: "D" Number of atoms: 3673 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3739 Chain: "E" Number of atoms: 3673 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3739 Chain: "F" Number of atoms: 3639 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 468, 3633 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 468, 3633 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 3703 Chain: "G" Number of atoms: 3668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 470, 3662 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 470, 3662 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 3734 Chain: "H" Number of atoms: 3640 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 467, 3634 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 23, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 467, 3634 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 23, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 3704 Chain: "I" Number of atoms: 3616 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 464, 3610 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 464, 3610 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3679 Chain: "J" Number of atoms: 3633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 466, 3627 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 466, 3627 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3698 Chain: "K" Number of atoms: 3648 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 444} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 444} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 3713 Chain: "L" Number of atoms: 3668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 470, 3662 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 470, 3662 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 3734 Chain: "X" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4782 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 32, 'TRANS': 578} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3642 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain: "Z" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1006 SG CYS A 134 94.319 18.849 67.092 1.00138.69 S ATOM 1058 SG CYS A 141 98.232 17.537 67.191 1.00120.54 S ATOM 4683 SG CYS B 134 139.320 25.510 64.633 1.00143.97 S ATOM 4735 SG CYS B 141 143.226 26.325 65.211 1.00114.99 S ATOM 8356 SG CYS C 134 176.816 52.385 62.609 1.00142.28 S ATOM 8408 SG CYS C 141 178.393 56.191 62.650 1.00120.87 S ATOM 12029 SG CYS D 134 192.237 95.890 60.986 1.00144.77 S ATOM 12081 SG CYS D 141 193.712 99.581 61.580 1.00126.42 S ATOM 15702 SG CYS E 134 185.946 141.119 60.653 1.00138.69 S ATOM 15754 SG CYS E 141 185.534 145.184 61.324 1.00117.05 S ATOM 19375 SG CYS F 134 158.993 178.231 62.249 1.00135.33 S ATOM 19427 SG CYS F 141 155.578 180.370 62.715 1.00121.33 S ATOM 23009 SG CYS G 134 116.184 195.994 63.541 1.00131.75 S ATOM 23061 SG CYS G 141 112.419 195.458 64.461 1.00104.53 S ATOM 26677 SG CYS H 134 70.334 188.867 66.152 1.00135.03 S ATOM 26729 SG CYS H 141 67.094 186.639 66.611 1.00114.42 S ATOM 30322 SG CYS I 134 33.548 160.276 68.134 1.00140.36 S ATOM 30374 SG CYS I 141 31.929 157.237 68.505 1.00124.62 S ATOM 33933 SG CYS J 134 17.712 117.240 69.338 1.00124.83 S ATOM 33985 SG CYS J 141 16.514 113.357 70.167 1.00117.81 S ATOM 37566 SG CYS K 134 24.285 72.175 69.736 1.00159.69 S ATOM 37618 SG CYS K 141 24.643 67.961 70.092 1.00119.96 S ATOM 41214 SG CYS L 134 52.078 36.040 68.777 1.00136.88 S ATOM 41266 SG CYS L 141 54.762 33.012 69.489 1.00116.90 S Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ACYS A 236 " occ=0.66 ... (10 atoms not shown) pdb=" SG BCYS A 236 " occ=0.34 residue: pdb=" N ACYS B 236 " occ=0.61 ... (10 atoms not shown) pdb=" SG BCYS B 236 " occ=0.39 residue: pdb=" N ACYS C 236 " occ=0.57 ... (10 atoms not shown) pdb=" SG BCYS C 236 " occ=0.43 residue: pdb=" N ACYS D 236 " occ=0.51 ... (10 atoms not shown) pdb=" SG BCYS D 236 " occ=0.49 residue: pdb=" N ACYS E 236 " occ=0.67 ... (10 atoms not shown) pdb=" SG BCYS E 236 " occ=0.33 residue: pdb=" N ACYS F 236 " occ=0.63 ... (10 atoms not shown) pdb=" SG BCYS F 236 " occ=0.37 residue: pdb=" N ACYS G 236 " occ=0.59 ... (10 atoms not shown) pdb=" SG BCYS G 236 " occ=0.41 residue: pdb=" N ACYS H 236 " occ=0.57 ... (10 atoms not shown) pdb=" SG BCYS H 236 " occ=0.43 residue: pdb=" N ACYS I 236 " occ=0.54 ... (10 atoms not shown) pdb=" SG BCYS I 236 " occ=0.46 residue: pdb=" N ACYS J 236 " occ=0.53 ... (10 atoms not shown) pdb=" SG BCYS J 236 " occ=0.47 residue: pdb=" N ACYS K 236 " occ=0.76 ... (10 atoms not shown) pdb=" SG BCYS K 236 " occ=0.24 residue: pdb=" N ACYS L 236 " occ=0.73 ... (10 atoms not shown) pdb=" SG BCYS L 236 " occ=0.27 Time building chain proxies: 35.47, per 1000 atoms: 0.67 Number of scatterers: 53135 At special positions: 0 Unit cell: (212.3, 211.2, 139.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 397 16.00 P 75 15.00 O 10061 8.00 N 9266 7.00 C 33324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 14.14 Conformation dependent library (CDL) restraints added in 9.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 134 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 134 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 134 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 134 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 134 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 134 " 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12742 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 213 helices and 77 sheets defined 29.9% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.91 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 39 through 54 removed outlier: 6.535A pdb=" N SER A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 49 " --> pdb=" O HIS A 45 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 89 through 103 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 158 through 168 removed outlier: 4.197A pdb=" N LYS A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 252 through 258 removed outlier: 4.154A pdb=" N TRP A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 384 through 402 removed outlier: 3.521A pdb=" N LYS A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET A 402 " --> pdb=" O CYS A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'B' and resid 15 through 21 Processing helix chain 'B' and resid 38 through 53 removed outlier: 3.570A pdb=" N PHE B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 103 Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.068A pdb=" N LYS B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 252 through 258 removed outlier: 4.040A pdb=" N TRP B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 removed outlier: 3.691A pdb=" N MET B 342 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 352 through 362 Processing helix chain 'B' and resid 381 through 402 removed outlier: 3.682A pdb=" N ILE B 384 " --> pdb=" O ASN B 381 " (cutoff:3.500A) Proline residue: B 385 - end of helix removed outlier: 3.532A pdb=" N ALA B 388 " --> pdb=" O PRO B 385 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS B 398 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 473 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 38 through 54 Processing helix chain 'C' and resid 89 through 102 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 158 through 168 removed outlier: 3.885A pdb=" N LYS C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 185 removed outlier: 3.699A pdb=" N TYR C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 181 through 185' Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 252 through 258 removed outlier: 4.030A pdb=" N TRP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 352 through 365 Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.554A pdb=" N ILE C 384 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Proline residue: C 385 - end of helix removed outlier: 3.548A pdb=" N ALA C 388 " --> pdb=" O PRO C 385 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 391 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 395 " --> pdb=" O SER C 392 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 400 " --> pdb=" O GLU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 471 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 38 through 53 removed outlier: 3.737A pdb=" N PHE D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 102 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 158 through 167 Processing helix chain 'D' and resid 181 through 185 removed outlier: 3.547A pdb=" N TYR D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 181 through 185' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 252 through 258 removed outlier: 4.030A pdb=" N TRP D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 352 through 363 Processing helix chain 'D' and resid 381 through 403 Proline residue: D 385 - end of helix removed outlier: 3.571A pdb=" N ALA D 388 " --> pdb=" O PRO D 385 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 391 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA D 395 " --> pdb=" O SER D 392 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N CYS D 398 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 399 " --> pdb=" O LYS D 396 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS D 400 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 403 " --> pdb=" O LYS D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 471 Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 38 through 54 removed outlier: 3.818A pdb=" N PHE E 43 " --> pdb=" O ASN E 39 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 71 Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.727A pdb=" N ALA E 103 " --> pdb=" O LYS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 158 through 168 removed outlier: 4.020A pdb=" N LYS E 168 " --> pdb=" O HIS E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 184 No H-bonds generated for 'chain 'E' and resid 181 through 184' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 252 through 258 removed outlier: 4.341A pdb=" N TRP E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 352 through 363 Processing helix chain 'E' and resid 381 through 400 Proline residue: E 385 - end of helix removed outlier: 3.532A pdb=" N ALA E 388 " --> pdb=" O PRO E 385 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN E 389 " --> pdb=" O VAL E 386 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS E 400 " --> pdb=" O GLU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 472 Processing helix chain 'F' and resid 13 through 21 removed outlier: 3.689A pdb=" N LYS F 16 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN F 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 54 removed outlier: 3.588A pdb=" N PHE F 43 " --> pdb=" O ASN F 39 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS F 49 " --> pdb=" O HIS F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 71 Processing helix chain 'F' and resid 89 through 102 Processing helix chain 'F' and resid 112 through 124 Processing helix chain 'F' and resid 158 through 168 removed outlier: 4.113A pdb=" N LYS F 168 " --> pdb=" O HIS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 184 No H-bonds generated for 'chain 'F' and resid 181 through 184' Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 252 through 258 removed outlier: 4.212A pdb=" N TRP F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 342 removed outlier: 3.561A pdb=" N MET F 342 " --> pdb=" O ILE F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 347 No H-bonds generated for 'chain 'F' and resid 345 through 347' Processing helix chain 'F' and resid 352 through 364 Processing helix chain 'F' and resid 381 through 402 removed outlier: 3.795A pdb=" N ILE F 384 " --> pdb=" O ASN F 381 " (cutoff:3.500A) Proline residue: F 385 - end of helix removed outlier: 3.638A pdb=" N ALA F 388 " --> pdb=" O PRO F 385 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE F 391 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA F 395 " --> pdb=" O SER F 392 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS F 400 " --> pdb=" O GLU F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 471 Processing helix chain 'G' and resid 14 through 21 Processing helix chain 'G' and resid 38 through 54 removed outlier: 3.695A pdb=" N PHE G 43 " --> pdb=" O ASN G 39 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS G 49 " --> pdb=" O HIS G 45 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 71 Processing helix chain 'G' and resid 89 through 102 Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 158 through 168 removed outlier: 4.064A pdb=" N LYS G 168 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 184 No H-bonds generated for 'chain 'G' and resid 181 through 184' Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 252 through 258 removed outlier: 4.056A pdb=" N TRP G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 342 removed outlier: 3.597A pdb=" N MET G 342 " --> pdb=" O ILE G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 347 No H-bonds generated for 'chain 'G' and resid 345 through 347' Processing helix chain 'G' and resid 352 through 364 Processing helix chain 'G' and resid 384 through 403 removed outlier: 3.587A pdb=" N LYS G 400 " --> pdb=" O LYS G 396 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP G 401 " --> pdb=" O GLU G 397 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET G 402 " --> pdb=" O CYS G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 473 removed outlier: 3.506A pdb=" N ARG G 467 " --> pdb=" O PRO G 463 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 21 Processing helix chain 'H' and resid 38 through 52 Processing helix chain 'H' and resid 68 through 71 Processing helix chain 'H' and resid 89 through 102 removed outlier: 3.826A pdb=" N SER H 102 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 158 through 168 removed outlier: 3.967A pdb=" N LYS H 168 " --> pdb=" O HIS H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 185 removed outlier: 3.734A pdb=" N TYR H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 181 through 185' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 252 through 258 removed outlier: 4.044A pdb=" N TRP H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 342 removed outlier: 3.566A pdb=" N GLN H 341 " --> pdb=" O THR H 337 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET H 342 " --> pdb=" O ILE H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 347 No H-bonds generated for 'chain 'H' and resid 345 through 347' Processing helix chain 'H' and resid 352 through 363 Processing helix chain 'H' and resid 381 through 403 Proline residue: H 385 - end of helix removed outlier: 3.581A pdb=" N ALA H 395 " --> pdb=" O SER H 392 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS H 398 " --> pdb=" O ALA H 395 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS H 400 " --> pdb=" O GLU H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 471 Processing helix chain 'I' and resid 13 through 21 removed outlier: 3.718A pdb=" N LYS I 16 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 54 removed outlier: 3.567A pdb=" N PHE I 43 " --> pdb=" O ASN I 39 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN I 53 " --> pdb=" O LYS I 49 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 70 No H-bonds generated for 'chain 'I' and resid 68 through 70' Processing helix chain 'I' and resid 89 through 103 Processing helix chain 'I' and resid 112 through 115 No H-bonds generated for 'chain 'I' and resid 112 through 115' Processing helix chain 'I' and resid 118 through 124 Processing helix chain 'I' and resid 158 through 167 Processing helix chain 'I' and resid 182 through 184 No H-bonds generated for 'chain 'I' and resid 182 through 184' Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 252 through 258 removed outlier: 4.183A pdb=" N TRP I 258 " --> pdb=" O LEU I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 342 removed outlier: 3.525A pdb=" N MET I 342 " --> pdb=" O ILE I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 352 through 363 Processing helix chain 'I' and resid 381 through 402 Proline residue: I 385 - end of helix removed outlier: 3.683A pdb=" N ALA I 388 " --> pdb=" O PRO I 385 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE I 391 " --> pdb=" O ALA I 388 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA I 395 " --> pdb=" O SER I 392 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS I 398 " --> pdb=" O ALA I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 471 Processing helix chain 'J' and resid 14 through 21 Processing helix chain 'J' and resid 38 through 54 removed outlier: 3.604A pdb=" N SER J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 71 Processing helix chain 'J' and resid 87 through 101 removed outlier: 4.630A pdb=" N GLU J 91 " --> pdb=" O ALA J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 124 Processing helix chain 'J' and resid 158 through 168 removed outlier: 4.122A pdb=" N LYS J 168 " --> pdb=" O HIS J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 185 removed outlier: 3.662A pdb=" N TYR J 185 " --> pdb=" O THR J 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 181 through 185' Processing helix chain 'J' and resid 193 through 195 No H-bonds generated for 'chain 'J' and resid 193 through 195' Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'J' and resid 252 through 258 removed outlier: 4.260A pdb=" N TRP J 258 " --> pdb=" O LEU J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 352 through 361 Processing helix chain 'J' and resid 381 through 400 Proline residue: J 385 - end of helix removed outlier: 3.531A pdb=" N ALA J 388 " --> pdb=" O PRO J 385 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE J 391 " --> pdb=" O ALA J 388 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA J 395 " --> pdb=" O SER J 392 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS J 400 " --> pdb=" O GLU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 472 Processing helix chain 'K' and resid 14 through 21 Processing helix chain 'K' and resid 38 through 54 removed outlier: 3.617A pdb=" N PHE K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU K 54 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 71 Processing helix chain 'K' and resid 89 through 102 Processing helix chain 'K' and resid 112 through 124 removed outlier: 3.520A pdb=" N VAL K 122 " --> pdb=" O ASP K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 168 removed outlier: 4.251A pdb=" N LYS K 168 " --> pdb=" O HIS K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 184 No H-bonds generated for 'chain 'K' and resid 181 through 184' Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'K' and resid 252 through 258 removed outlier: 4.216A pdb=" N TRP K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 342 removed outlier: 3.520A pdb=" N MET K 342 " --> pdb=" O ILE K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 347 No H-bonds generated for 'chain 'K' and resid 345 through 347' Processing helix chain 'K' and resid 352 through 364 Processing helix chain 'K' and resid 381 through 403 Proline residue: K 385 - end of helix removed outlier: 3.576A pdb=" N ALA K 388 " --> pdb=" O PRO K 385 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE K 391 " --> pdb=" O ALA K 388 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA K 395 " --> pdb=" O SER K 392 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS K 398 " --> pdb=" O ALA K 395 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 472 Processing helix chain 'L' and resid 14 through 21 Processing helix chain 'L' and resid 38 through 53 removed outlier: 3.538A pdb=" N SER L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS L 49 " --> pdb=" O HIS L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 102 Processing helix chain 'L' and resid 112 through 124 Processing helix chain 'L' and resid 158 through 168 removed outlier: 4.090A pdb=" N LYS L 168 " --> pdb=" O HIS L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 184 No H-bonds generated for 'chain 'L' and resid 182 through 184' Processing helix chain 'L' and resid 193 through 195 No H-bonds generated for 'chain 'L' and resid 193 through 195' Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 252 through 258 removed outlier: 4.004A pdb=" N TRP L 258 " --> pdb=" O LEU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 336 through 342 removed outlier: 3.507A pdb=" N MET L 342 " --> pdb=" O ILE L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 345 through 347 No H-bonds generated for 'chain 'L' and resid 345 through 347' Processing helix chain 'L' and resid 352 through 363 Processing helix chain 'L' and resid 381 through 403 removed outlier: 3.673A pdb=" N ILE L 384 " --> pdb=" O ASN L 381 " (cutoff:3.500A) Proline residue: L 385 - end of helix removed outlier: 3.633A pdb=" N ALA L 388 " --> pdb=" O PRO L 385 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE L 391 " --> pdb=" O ALA L 388 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA L 395 " --> pdb=" O SER L 392 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG L 399 " --> pdb=" O LYS L 396 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS L 400 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 473 Processing helix chain 'X' and resid 43 through 54 removed outlier: 3.556A pdb=" N GLU X 54 " --> pdb=" O LYS X 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 83 removed outlier: 3.705A pdb=" N TYR X 64 " --> pdb=" O ASN X 60 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU X 82 " --> pdb=" O HIS X 78 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY X 83 " --> pdb=" O ARG X 79 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 132 Processing helix chain 'X' and resid 136 through 138 No H-bonds generated for 'chain 'X' and resid 136 through 138' Processing helix chain 'X' and resid 146 through 152 Processing helix chain 'X' and resid 166 through 168 No H-bonds generated for 'chain 'X' and resid 166 through 168' Processing helix chain 'X' and resid 195 through 201 Processing helix chain 'X' and resid 215 through 231 Processing helix chain 'X' and resid 238 through 243 removed outlier: 3.593A pdb=" N SER X 243 " --> pdb=" O ARG X 239 " (cutoff:3.500A) Processing helix chain 'X' and resid 250 through 259 removed outlier: 3.525A pdb=" N LYS X 259 " --> pdb=" O THR X 255 " (cutoff:3.500A) Processing helix chain 'X' and resid 262 through 271 removed outlier: 3.875A pdb=" N LYS X 271 " --> pdb=" O ALA X 267 " (cutoff:3.500A) Processing helix chain 'X' and resid 278 through 280 No H-bonds generated for 'chain 'X' and resid 278 through 280' Processing helix chain 'X' and resid 319 through 322 No H-bonds generated for 'chain 'X' and resid 319 through 322' Processing helix chain 'X' and resid 327 through 337 removed outlier: 3.515A pdb=" N VAL X 337 " --> pdb=" O ARG X 333 " (cutoff:3.500A) Processing helix chain 'X' and resid 350 through 356 Processing helix chain 'X' and resid 381 through 394 removed outlier: 3.925A pdb=" N THR X 386 " --> pdb=" O LEU X 383 " (cutoff:3.500A) Processing helix chain 'X' and resid 398 through 408 removed outlier: 3.572A pdb=" N ASP X 402 " --> pdb=" O GLN X 398 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU X 403 " --> pdb=" O PRO X 399 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA X 407 " --> pdb=" O LEU X 403 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE X 408 " --> pdb=" O ILE X 404 " (cutoff:3.500A) Processing helix chain 'X' and resid 436 through 454 removed outlier: 6.813A pdb=" N GLU X 453 " --> pdb=" O ARG X 449 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG X 454 " --> pdb=" O VAL X 450 " (cutoff:3.500A) Processing helix chain 'X' and resid 477 through 485 removed outlier: 4.157A pdb=" N THR X 485 " --> pdb=" O ALA X 481 " (cutoff:3.500A) Processing helix chain 'X' and resid 525 through 533 removed outlier: 4.158A pdb=" N GLY X 533 " --> pdb=" O LEU X 529 " (cutoff:3.500A) Processing helix chain 'X' and resid 545 through 558 Processing helix chain 'X' and resid 563 through 574 Processing helix chain 'X' and resid 580 through 591 removed outlier: 4.036A pdb=" N SER X 591 " --> pdb=" O ALA X 587 " (cutoff:3.500A) Processing helix chain 'X' and resid 595 through 599 removed outlier: 3.703A pdb=" N LYS X 598 " --> pdb=" O ASN X 595 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU X 599 " --> pdb=" O PHE X 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 595 through 599' Processing helix chain 'Y' and resid 6 through 8 No H-bonds generated for 'chain 'Y' and resid 6 through 8' Processing helix chain 'Y' and resid 29 through 33 Processing helix chain 'Y' and resid 36 through 48 removed outlier: 3.526A pdb=" N SER Y 39 " --> pdb=" O GLN Y 36 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU Y 40 " --> pdb=" O LYS Y 37 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE Y 41 " --> pdb=" O LEU Y 38 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS Y 42 " --> pdb=" O SER Y 39 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA Y 43 " --> pdb=" O LEU Y 40 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL Y 48 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 79 through 108 removed outlier: 3.631A pdb=" N GLN Y 83 " --> pdb=" O PRO Y 79 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER Y 84 " --> pdb=" O GLU Y 80 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL Y 92 " --> pdb=" O SER Y 88 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU Y 97 " --> pdb=" O TYR Y 93 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE Y 98 " --> pdb=" O ASN Y 94 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL Y 99 " --> pdb=" O GLU Y 95 " (cutoff:3.500A) Processing helix chain 'Y' and resid 117 through 119 No H-bonds generated for 'chain 'Y' and resid 117 through 119' Processing helix chain 'Y' and resid 155 through 158 No H-bonds generated for 'chain 'Y' and resid 155 through 158' Processing helix chain 'Y' and resid 163 through 165 No H-bonds generated for 'chain 'Y' and resid 163 through 165' Processing helix chain 'Y' and resid 167 through 171 Processing helix chain 'Y' and resid 192 through 197 removed outlier: 3.692A pdb=" N ILE Y 196 " --> pdb=" O LYS Y 192 " (cutoff:3.500A) Processing helix chain 'Y' and resid 211 through 224 removed outlier: 3.659A pdb=" N ILE Y 217 " --> pdb=" O ASN Y 213 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR Y 218 " --> pdb=" O CYS Y 214 " (cutoff:3.500A) Processing helix chain 'Y' and resid 234 through 239 Processing helix chain 'Y' and resid 259 through 269 removed outlier: 3.551A pdb=" N VAL Y 269 " --> pdb=" O LEU Y 265 " (cutoff:3.500A) Processing helix chain 'Y' and resid 316 through 319 Processing helix chain 'Y' and resid 321 through 324 No H-bonds generated for 'chain 'Y' and resid 321 through 324' Processing helix chain 'Y' and resid 361 through 370 removed outlier: 4.864A pdb=" N LYS Y 365 " --> pdb=" O GLY Y 362 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN Y 368 " --> pdb=" O LYS Y 365 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE Y 369 " --> pdb=" O GLN Y 366 " (cutoff:3.500A) Processing helix chain 'Y' and resid 410 through 412 No H-bonds generated for 'chain 'Y' and resid 410 through 412' Processing helix chain 'Y' and resid 433 through 435 No H-bonds generated for 'chain 'Y' and resid 433 through 435' Processing helix chain 'Y' and resid 448 through 450 No H-bonds generated for 'chain 'Y' and resid 448 through 450' Processing helix chain 'Y' and resid 453 through 459 removed outlier: 3.883A pdb=" N MET Y 458 " --> pdb=" O HIS Y 454 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 4 through 6 removed outlier: 3.540A pdb=" N VAL A 6 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.786A pdb=" N ILE A 61 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL A 81 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASP A 63 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 147 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE A 64 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE A 149 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU A 172 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N TYR A 150 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR A 174 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 177 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 280 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ARG A 289 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N THR A 278 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR A 291 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N CYS A 276 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N SER A 293 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N CYS A 274 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 189 through 192 removed outlier: 3.523A pdb=" N TRP A 199 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 303 through 308 removed outlier: 3.786A pdb=" N THR A 437 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 324 through 333 Processing sheet with id= F, first strand: chain 'B' and resid 4 through 6 Processing sheet with id= G, first strand: chain 'B' and resid 77 through 80 removed outlier: 6.893A pdb=" N VAL B 147 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B 172 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N TYR B 150 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR B 174 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 177 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 280 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG B 289 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N THR B 278 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR B 291 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N CYS B 276 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N SER B 293 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N CYS B 274 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 264 " --> pdb=" O CYS B 274 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 189 through 192 Processing sheet with id= I, first strand: chain 'B' and resid 303 through 308 removed outlier: 3.894A pdb=" N THR B 437 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 324 through 334 Processing sheet with id= K, first strand: chain 'B' and resid 365 through 368 Processing sheet with id= L, first strand: chain 'C' and resid 4 through 6 Processing sheet with id= M, first strand: chain 'C' and resid 77 through 81 removed outlier: 6.975A pdb=" N VAL C 147 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE C 64 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE C 149 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU C 172 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N TYR C 150 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR C 174 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY C 177 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL C 280 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG C 289 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N THR C 278 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N THR C 291 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N CYS C 276 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N SER C 293 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N CYS C 274 " --> pdb=" O SER C 293 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 264 " --> pdb=" O CYS C 274 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 189 through 192 Processing sheet with id= O, first strand: chain 'C' and resid 303 through 308 removed outlier: 4.053A pdb=" N THR C 437 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 324 through 334 Processing sheet with id= Q, first strand: chain 'D' and resid 4 through 6 Processing sheet with id= R, first strand: chain 'D' and resid 77 through 81 removed outlier: 6.646A pdb=" N VAL D 147 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE D 64 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE D 149 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU D 172 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 177 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL D 280 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG D 289 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N THR D 278 " --> pdb=" O ARG D 289 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 189 through 192 Processing sheet with id= T, first strand: chain 'D' and resid 263 through 266 removed outlier: 3.526A pdb=" N PHE D 264 " --> pdb=" O CYS D 274 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 303 through 308 removed outlier: 3.915A pdb=" N THR D 437 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 324 through 334 Processing sheet with id= W, first strand: chain 'D' and resid 365 through 369 Processing sheet with id= X, first strand: chain 'E' and resid 3 through 6 removed outlier: 6.470A pdb=" N GLU E 26 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL E 6 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU E 28 " --> pdb=" O VAL E 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 77 through 81 removed outlier: 6.769A pdb=" N VAL E 147 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE E 64 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE E 149 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU E 172 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N TYR E 150 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N TYR E 174 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY E 177 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL E 280 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N THR E 278 " --> pdb=" O ARG E 289 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 189 through 192 Processing sheet with id= AA, first strand: chain 'E' and resid 263 through 267 removed outlier: 3.529A pdb=" N PHE E 264 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS E 274 " --> pdb=" O PHE E 264 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 303 through 308 removed outlier: 3.877A pdb=" N THR E 437 " --> pdb=" O HIS E 308 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 324 through 334 Processing sheet with id= AD, first strand: chain 'E' and resid 365 through 368 Processing sheet with id= AE, first strand: chain 'F' and resid 4 through 6 Processing sheet with id= AF, first strand: chain 'F' and resid 78 through 81 removed outlier: 6.811A pdb=" N ILE F 61 " --> pdb=" O HIS F 79 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL F 81 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP F 63 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL F 147 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ILE F 64 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE F 149 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU F 172 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR F 150 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR F 174 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY F 177 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR F 285 " --> pdb=" O CYS F 282 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL F 280 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG F 289 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR F 278 " --> pdb=" O ARG F 289 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N THR F 291 " --> pdb=" O CYS F 276 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N CYS F 276 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N SER F 293 " --> pdb=" O CYS F 274 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N CYS F 274 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 189 through 192 removed outlier: 3.604A pdb=" N TRP F 199 " --> pdb=" O GLY F 190 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 303 through 308 removed outlier: 3.950A pdb=" N THR F 437 " --> pdb=" O HIS F 308 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 324 through 334 Processing sheet with id= AJ, first strand: chain 'G' and resid 4 through 6 Processing sheet with id= AK, first strand: chain 'G' and resid 78 through 81 removed outlier: 6.839A pdb=" N ILE G 61 " --> pdb=" O HIS G 79 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL G 81 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP G 63 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL G 147 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE G 64 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE G 149 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU G 172 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N TYR G 150 " --> pdb=" O LEU G 172 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TYR G 174 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY G 177 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL G 280 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG G 289 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N THR G 278 " --> pdb=" O ARG G 289 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR G 291 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N CYS G 276 " --> pdb=" O THR G 291 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N SER G 293 " --> pdb=" O CYS G 274 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N CYS G 274 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 189 through 192 Processing sheet with id= AM, first strand: chain 'G' and resid 303 through 308 removed outlier: 3.875A pdb=" N THR G 437 " --> pdb=" O HIS G 308 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 324 through 334 Processing sheet with id= AO, first strand: chain 'H' and resid 4 through 6 Processing sheet with id= AP, first strand: chain 'H' and resid 78 through 81 removed outlier: 6.621A pdb=" N ILE H 61 " --> pdb=" O HIS H 79 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL H 81 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP H 63 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL H 147 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ILE H 64 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE H 149 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU H 172 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N TYR H 150 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYR H 174 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL H 280 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG H 289 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N THR H 278 " --> pdb=" O ARG H 289 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N THR H 291 " --> pdb=" O CYS H 276 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N CYS H 276 " --> pdb=" O THR H 291 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SER H 293 " --> pdb=" O CYS H 274 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N CYS H 274 " --> pdb=" O SER H 293 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS H 274 " --> pdb=" O PHE H 264 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 189 through 192 Processing sheet with id= AR, first strand: chain 'H' and resid 303 through 308 removed outlier: 3.853A pdb=" N THR H 437 " --> pdb=" O HIS H 308 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 324 through 334 Processing sheet with id= AT, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.750A pdb=" N VAL I 6 " --> pdb=" O GLU I 28 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'I' and resid 77 through 81 removed outlier: 6.893A pdb=" N VAL I 147 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE I 64 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE I 149 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU I 172 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N TYR I 150 " --> pdb=" O LEU I 172 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TYR I 174 " --> pdb=" O TYR I 150 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY I 177 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL I 280 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG I 289 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N THR I 278 " --> pdb=" O ARG I 289 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR I 291 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N CYS I 276 " --> pdb=" O THR I 291 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N SER I 293 " --> pdb=" O CYS I 274 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N CYS I 274 " --> pdb=" O SER I 293 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE I 264 " --> pdb=" O CYS I 274 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'I' and resid 189 through 192 Processing sheet with id= AW, first strand: chain 'I' and resid 303 through 308 removed outlier: 3.864A pdb=" N THR I 437 " --> pdb=" O HIS I 308 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'I' and resid 324 through 334 Processing sheet with id= AY, first strand: chain 'J' and resid 4 through 6 Processing sheet with id= AZ, first strand: chain 'J' and resid 77 through 80 removed outlier: 7.149A pdb=" N VAL J 147 " --> pdb=" O LEU J 62 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU J 172 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N TYR J 150 " --> pdb=" O LEU J 172 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR J 174 " --> pdb=" O TYR J 150 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY J 177 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL J 280 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ARG J 289 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N THR J 278 " --> pdb=" O ARG J 289 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'J' and resid 189 through 192 Processing sheet with id= BB, first strand: chain 'J' and resid 263 through 266 removed outlier: 3.522A pdb=" N PHE J 264 " --> pdb=" O CYS J 274 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'J' and resid 303 through 308 removed outlier: 3.895A pdb=" N THR J 437 " --> pdb=" O HIS J 308 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'J' and resid 324 through 334 Processing sheet with id= BE, first strand: chain 'K' and resid 4 through 6 Processing sheet with id= BF, first strand: chain 'K' and resid 61 through 64 Processing sheet with id= BG, first strand: chain 'K' and resid 147 through 151 removed outlier: 6.538A pdb=" N LEU K 172 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR K 150 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR K 174 " --> pdb=" O TYR K 150 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY K 177 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL K 280 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG K 289 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR K 278 " --> pdb=" O ARG K 289 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR K 291 " --> pdb=" O CYS K 276 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N CYS K 276 " --> pdb=" O THR K 291 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N SER K 293 " --> pdb=" O CYS K 274 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N CYS K 274 " --> pdb=" O SER K 293 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS K 274 " --> pdb=" O PHE K 264 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE K 264 " --> pdb=" O CYS K 274 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'K' and resid 189 through 192 Processing sheet with id= BI, first strand: chain 'K' and resid 303 through 308 removed outlier: 3.860A pdb=" N THR K 437 " --> pdb=" O HIS K 308 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'K' and resid 324 through 334 Processing sheet with id= BK, first strand: chain 'K' and resid 365 through 368 removed outlier: 4.070A pdb=" N ILE K 366 " --> pdb=" O GLN K 373 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= BM, first strand: chain 'L' and resid 77 through 81 removed outlier: 6.615A pdb=" N VAL L 147 " --> pdb=" O LEU L 62 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE L 64 " --> pdb=" O VAL L 147 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE L 149 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU L 172 " --> pdb=" O ALA L 148 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR L 150 " --> pdb=" O LEU L 172 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR L 174 " --> pdb=" O TYR L 150 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY L 177 " --> pdb=" O VAL L 286 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL L 280 " --> pdb=" O VAL L 287 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG L 289 " --> pdb=" O THR L 278 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR L 278 " --> pdb=" O ARG L 289 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR L 291 " --> pdb=" O CYS L 276 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N CYS L 276 " --> pdb=" O THR L 291 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N SER L 293 " --> pdb=" O CYS L 274 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N CYS L 274 " --> pdb=" O SER L 293 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'L' and resid 189 through 192 Processing sheet with id= BO, first strand: chain 'L' and resid 303 through 308 removed outlier: 3.721A pdb=" N THR L 437 " --> pdb=" O HIS L 308 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'L' and resid 324 through 334 Processing sheet with id= BQ, first strand: chain 'L' and resid 366 through 368 removed outlier: 6.040A pdb=" N VAL L 368 " --> pdb=" O THR L 372 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N THR L 372 " --> pdb=" O VAL L 368 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'X' and resid 26 through 29 removed outlier: 3.569A pdb=" N ILE X 26 " --> pdb=" O THR X 101 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'X' and resid 176 through 179 Processing sheet with id= BT, first strand: chain 'X' and resid 312 through 314 removed outlier: 6.494A pdb=" N SER X 412 " --> pdb=" O PHE X 286 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N MET X 288 " --> pdb=" O SER X 412 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N CYS X 414 " --> pdb=" O MET X 288 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'X' and resid 342 through 344 removed outlier: 6.542A pdb=" N ALA X 461 " --> pdb=" O HIS X 343 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'X' and resid 508 through 512 Processing sheet with id= BW, first strand: chain 'Y' and resid 24 through 28 Processing sheet with id= BX, first strand: chain 'Y' and resid 249 through 251 Processing sheet with id= BY, first strand: chain 'Y' and resid 390 through 392 removed outlier: 3.653A pdb=" N VAL Y 422 " --> pdb=" O VAL Y 390 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA Y 392 " --> pdb=" O VAL Y 422 " (cutoff:3.500A) No H-bonds generated for sheet with id= BY 1687 hydrogen bonds defined for protein. 4359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.49 Time building geometry restraints manager: 15.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8574 1.31 - 1.44: 14247 1.44 - 1.56: 30725 1.56 - 1.69: 157 1.69 - 1.82: 593 Bond restraints: 54296 Sorted by residual: bond pdb=" C1' ATP B1003 " pdb=" C2' ATP B1003 " ideal model delta sigma weight residual 1.531 1.300 0.231 1.20e-02 6.94e+03 3.70e+02 bond pdb=" C1' ATP H1002 " pdb=" C2' ATP H1002 " ideal model delta sigma weight residual 1.531 1.300 0.231 1.20e-02 6.94e+03 3.69e+02 bond pdb=" C1' ATP F1003 " pdb=" C2' ATP F1003 " ideal model delta sigma weight residual 1.531 1.300 0.231 1.20e-02 6.94e+03 3.69e+02 bond pdb=" C1' ATP G1002 " pdb=" C2' ATP G1002 " ideal model delta sigma weight residual 1.531 1.301 0.230 1.20e-02 6.94e+03 3.68e+02 bond pdb=" C1' ATP I1002 " pdb=" C2' ATP I1002 " ideal model delta sigma weight residual 1.531 1.301 0.230 1.20e-02 6.94e+03 3.68e+02 ... (remaining 54291 not shown) Histogram of bond angle deviations from ideal: 99.77 - 107.10: 1851 107.10 - 114.43: 32742 114.43 - 121.76: 26289 121.76 - 129.09: 12545 129.09 - 136.41: 431 Bond angle restraints: 73858 Sorted by residual: angle pdb=" PB ATP L1002 " pdb=" O3B ATP L1002 " pdb=" PG ATP L1002 " ideal model delta sigma weight residual 139.87 123.70 16.17 1.00e+00 1.00e+00 2.61e+02 angle pdb=" PB ATP F1003 " pdb=" O3B ATP F1003 " pdb=" PG ATP F1003 " ideal model delta sigma weight residual 139.87 123.73 16.14 1.00e+00 1.00e+00 2.61e+02 angle pdb=" PB ATP B1003 " pdb=" O3B ATP B1003 " pdb=" PG ATP B1003 " ideal model delta sigma weight residual 139.87 123.76 16.11 1.00e+00 1.00e+00 2.60e+02 angle pdb=" PB ATP D1003 " pdb=" O3B ATP D1003 " pdb=" PG ATP D1003 " ideal model delta sigma weight residual 139.87 123.77 16.10 1.00e+00 1.00e+00 2.59e+02 angle pdb=" PB ATP C1003 " pdb=" O3B ATP C1003 " pdb=" PG ATP C1003 " ideal model delta sigma weight residual 139.87 123.78 16.09 1.00e+00 1.00e+00 2.59e+02 ... (remaining 73853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 32175 35.54 - 71.08: 497 71.08 - 106.62: 44 106.62 - 142.16: 17 142.16 - 177.70: 23 Dihedral angle restraints: 32756 sinusoidal: 13056 harmonic: 19700 Sorted by residual: dihedral pdb=" C8 GTP F1002 " pdb=" C1' GTP F1002 " pdb=" N9 GTP F1002 " pdb=" O4' GTP F1002 " ideal model delta sinusoidal sigma weight residual 104.59 -73.11 177.70 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2G GTP E1002 " pdb=" O3B GTP E1002 " pdb=" PG GTP E1002 " pdb=" PB GTP E1002 " ideal model delta sinusoidal sigma weight residual 177.30 -5.49 -177.21 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP D1002 " pdb=" C1' GTP D1002 " pdb=" N9 GTP D1002 " pdb=" O4' GTP D1002 " ideal model delta sinusoidal sigma weight residual 104.59 -71.13 175.72 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 32753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 7372 0.065 - 0.130: 969 0.130 - 0.195: 12 0.195 - 0.260: 1 0.260 - 0.325: 12 Chirality restraints: 8366 Sorted by residual: chirality pdb=" C2' ATP D1003 " pdb=" C1' ATP D1003 " pdb=" C3' ATP D1003 " pdb=" O2' ATP D1003 " both_signs ideal model delta sigma weight residual False -2.68 -2.35 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C2' ATP E1003 " pdb=" C1' ATP E1003 " pdb=" C3' ATP E1003 " pdb=" O2' ATP E1003 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C2' ATP A1002 " pdb=" C1' ATP A1002 " pdb=" C3' ATP A1002 " pdb=" O2' ATP A1002 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 8363 not shown) Planarity restraints: 9280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 2 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO D 3 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 3 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 3 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 125 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.56e+00 pdb=" N PRO B 126 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP Y 351 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO Y 352 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO Y 352 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO Y 352 " 0.033 5.00e-02 4.00e+02 ... (remaining 9277 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 593 2.67 - 3.23: 45584 3.23 - 3.79: 71736 3.79 - 4.34: 100580 4.34 - 4.90: 171083 Nonbonded interactions: 389576 Sorted by model distance: nonbonded pdb=" OE2 GLU F 129 " pdb="ZN ZN F1001 " model vdw 2.113 2.230 nonbonded pdb=" OE2 GLU B 412 " pdb=" OG1 THR B 414 " model vdw 2.150 2.440 nonbonded pdb=" OG1 THR B 130 " pdb=" O PHE B 133 " model vdw 2.178 2.440 nonbonded pdb=" OG1 THR J 130 " pdb=" O PHE J 133 " model vdw 2.186 2.440 nonbonded pdb=" OE2 GLU X 567 " pdb=" OG1 THR X 580 " model vdw 2.213 2.440 ... (remaining 389571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 235 or resid 237 through 268 or (resid 269 and ( \ name N or name CA or name C or name O or name CB )) or resid 270 through 373 or \ (resid 374 and (name N or name CA or name C or name O or name CB )) or resid 375 \ through 414 or resid 422 through 472 or resid 1001)) selection = (chain 'B' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 414 or \ resid 422 through 472 or resid 1001)) selection = (chain 'C' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 414 or \ resid 422 through 472 or resid 1001)) selection = (chain 'D' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 414 or \ resid 422 through 472 or resid 1001)) selection = (chain 'E' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 414 or \ resid 422 through 472 or resid 1001)) selection = (chain 'F' and (resid 3 through 235 or resid 237 through 472 or resid 1001)) selection = (chain 'G' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 414 or \ resid 422 through 472 or resid 1001)) selection = (chain 'H' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 472 or \ resid 1001)) selection = (chain 'I' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 472 or \ resid 1001)) selection = (chain 'J' and (resid 3 through 235 or resid 237 through 414 or resid 422 throug \ h 472 or resid 1001)) selection = (chain 'K' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 414 or \ resid 422 through 472 or resid 1001)) selection = (chain 'L' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 414 or \ resid 422 through 472 or resid 1001)) } 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=0.24 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 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: 0.050 Extract box with map and model: 14.760 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 126.310 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.010 0.231 54296 Z= 0.650 Angle : 0.719 16.171 73858 Z= 0.464 Chirality : 0.043 0.325 8366 Planarity : 0.005 0.075 9280 Dihedral : 14.980 177.702 20014 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.15 % Rotamer: Outliers : 0.04 % Allowed : 0.09 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -0.63 (0.10), residues: 6688 helix: 1.09 (0.12), residues: 1926 sheet: 0.84 (0.15), residues: 1225 loop : -1.84 (0.09), residues: 3537 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 522 time to evaluate : 4.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 523 average time/residue: 1.5483 time to fit residues: 992.9457 Evaluate side-chains 393 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 4.721 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 562 optimal weight: 9.9990 chunk 504 optimal weight: 0.9990 chunk 280 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 340 optimal weight: 10.0000 chunk 269 optimal weight: 6.9990 chunk 522 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 388 optimal weight: 1.9990 chunk 604 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN D 259 HIS F 377 ASN G 95 ASN I 441 GLN L 389 GLN X 65 GLN X 439 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54296 Z= 0.225 Angle : 0.617 15.756 73858 Z= 0.307 Chirality : 0.044 0.285 8366 Planarity : 0.005 0.069 9280 Dihedral : 11.991 178.138 7593 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.07 % Favored : 94.87 % Rotamer: Outliers : 0.84 % Allowed : 6.22 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -0.56 (0.10), residues: 6688 helix: 1.35 (0.12), residues: 1899 sheet: 0.77 (0.15), residues: 1248 loop : -1.89 (0.09), residues: 3541 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 399 time to evaluate : 4.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 16 residues processed: 423 average time/residue: 1.4808 time to fit residues: 777.7487 Evaluate side-chains 387 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 371 time to evaluate : 4.569 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 7 average time/residue: 0.7353 time to fit residues: 13.6604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 336 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 503 optimal weight: 0.0070 chunk 411 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 605 optimal weight: 10.0000 chunk 654 optimal weight: 50.0000 chunk 539 optimal weight: 2.9990 chunk 600 optimal weight: 0.0980 chunk 206 optimal weight: 3.9990 chunk 486 optimal weight: 3.9990 overall best weight: 1.8204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN C 441 GLN F 377 ASN G 95 ASN G 364 GLN L 389 GLN Y 47 GLN Y 104 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 54296 Z= 0.244 Angle : 0.612 15.862 73858 Z= 0.303 Chirality : 0.044 0.292 8366 Planarity : 0.005 0.064 9280 Dihedral : 11.529 178.976 7593 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.05 % Favored : 94.89 % Rotamer: Outliers : 0.76 % Allowed : 7.90 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -0.59 (0.10), residues: 6688 helix: 1.41 (0.13), residues: 1917 sheet: 0.71 (0.15), residues: 1203 loop : -1.93 (0.09), residues: 3568 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 383 time to evaluate : 4.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 21 residues processed: 408 average time/residue: 1.4475 time to fit residues: 737.7243 Evaluate side-chains 387 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 366 time to evaluate : 4.546 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 12 residues processed: 10 average time/residue: 0.5914 time to fit residues: 15.4267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 598 optimal weight: 3.9990 chunk 455 optimal weight: 0.8980 chunk 314 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 289 optimal weight: 0.9990 chunk 406 optimal weight: 0.9980 chunk 608 optimal weight: 8.9990 chunk 643 optimal weight: 0.4980 chunk 317 optimal weight: 2.9990 chunk 576 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN C 441 GLN F 377 ASN F 389 GLN ** L 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 47 GLN Y 298 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 54296 Z= 0.160 Angle : 0.567 15.363 73858 Z= 0.276 Chirality : 0.042 0.268 8366 Planarity : 0.005 0.062 9280 Dihedral : 11.295 178.984 7593 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.44 % Rotamer: Outliers : 0.84 % Allowed : 8.62 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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 (0.10), residues: 6688 helix: 1.46 (0.13), residues: 1924 sheet: 0.77 (0.14), residues: 1239 loop : -1.87 (0.10), residues: 3525 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 382 time to evaluate : 4.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 17 residues processed: 413 average time/residue: 1.4276 time to fit residues: 743.4130 Evaluate side-chains 382 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 365 time to evaluate : 4.597 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 5 average time/residue: 0.5567 time to fit residues: 10.5912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 536 optimal weight: 0.9980 chunk 365 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 479 optimal weight: 2.9990 chunk 265 optimal weight: 6.9990 chunk 549 optimal weight: 0.7980 chunk 444 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 328 optimal weight: 6.9990 chunk 577 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN C 441 GLN F 377 ASN I 157 HIS ** L 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 54296 Z= 0.194 Angle : 0.581 15.617 73858 Z= 0.284 Chirality : 0.043 0.283 8366 Planarity : 0.005 0.062 9280 Dihedral : 11.159 179.994 7593 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.10 % Favored : 94.84 % Rotamer: Outliers : 0.81 % Allowed : 9.47 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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 (0.10), residues: 6688 helix: 1.53 (0.13), residues: 1919 sheet: 0.76 (0.14), residues: 1220 loop : -1.86 (0.10), residues: 3549 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 366 time to evaluate : 4.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 20 residues processed: 398 average time/residue: 1.4387 time to fit residues: 721.5938 Evaluate side-chains 378 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 358 time to evaluate : 4.604 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 7 average time/residue: 0.6601 time to fit residues: 13.1575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 216 optimal weight: 0.8980 chunk 579 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 377 optimal weight: 0.3980 chunk 158 optimal weight: 6.9990 chunk 644 optimal weight: 10.0000 chunk 534 optimal weight: 8.9990 chunk 298 optimal weight: 4.9990 chunk 53 optimal weight: 0.0670 chunk 213 optimal weight: 5.9990 chunk 338 optimal weight: 7.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS B 375 ASN C 441 GLN F 377 ASN L 389 GLN Y 47 GLN Y 442 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 54296 Z= 0.143 Angle : 0.555 15.117 73858 Z= 0.268 Chirality : 0.042 0.260 8366 Planarity : 0.005 0.060 9280 Dihedral : 10.913 179.846 7593 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.09 % Favored : 95.85 % Rotamer: Outliers : 0.65 % Allowed : 9.82 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.10), residues: 6688 helix: 1.56 (0.13), residues: 1922 sheet: 0.86 (0.14), residues: 1246 loop : -1.82 (0.10), residues: 3520 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 379 time to evaluate : 4.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 17 residues processed: 405 average time/residue: 1.4337 time to fit residues: 732.9133 Evaluate side-chains 375 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 358 time to evaluate : 4.540 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.4042 time to fit residues: 8.3332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 621 optimal weight: 20.0000 chunk 72 optimal weight: 0.7980 chunk 367 optimal weight: 0.9980 chunk 470 optimal weight: 0.8980 chunk 364 optimal weight: 3.9990 chunk 542 optimal weight: 6.9990 chunk 359 optimal weight: 3.9990 chunk 641 optimal weight: 7.9990 chunk 401 optimal weight: 2.9990 chunk 391 optimal weight: 0.8980 chunk 296 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN C 441 GLN E 375 ASN F 377 ASN ** L 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 442 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54296 Z= 0.196 Angle : 0.582 15.557 73858 Z= 0.284 Chirality : 0.043 0.286 8366 Planarity : 0.005 0.060 9280 Dihedral : 10.777 179.672 7593 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 0.74 % Allowed : 10.36 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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 (0.10), residues: 6688 helix: 1.63 (0.13), residues: 1922 sheet: 0.82 (0.14), residues: 1256 loop : -1.85 (0.10), residues: 3510 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 365 time to evaluate : 4.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 23 residues processed: 394 average time/residue: 1.4255 time to fit residues: 710.9758 Evaluate side-chains 377 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 354 time to evaluate : 4.617 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 16 residues processed: 7 average time/residue: 0.5519 time to fit residues: 12.5867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 397 optimal weight: 0.5980 chunk 256 optimal weight: 0.9990 chunk 383 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 408 optimal weight: 5.9990 chunk 437 optimal weight: 6.9990 chunk 317 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 504 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN C 441 GLN ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 ASN F 377 ASN ** L 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 54296 Z= 0.214 Angle : 0.592 15.865 73858 Z= 0.289 Chirality : 0.043 0.294 8366 Planarity : 0.005 0.060 9280 Dihedral : 10.665 179.529 7593 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.93 % Favored : 94.99 % Rotamer: Outliers : 0.63 % Allowed : 10.61 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.10), residues: 6688 helix: 1.60 (0.13), residues: 1923 sheet: 0.82 (0.14), residues: 1228 loop : -1.84 (0.10), residues: 3537 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 365 time to evaluate : 4.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 24 residues processed: 390 average time/residue: 1.4578 time to fit residues: 715.1156 Evaluate side-chains 381 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 357 time to evaluate : 4.589 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 6 average time/residue: 0.9340 time to fit residues: 13.8770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 583 optimal weight: 3.9990 chunk 614 optimal weight: 5.9990 chunk 561 optimal weight: 7.9990 chunk 598 optimal weight: 4.9990 chunk 360 optimal weight: 0.9990 chunk 260 optimal weight: 4.9990 chunk 469 optimal weight: 0.2980 chunk 183 optimal weight: 5.9990 chunk 540 optimal weight: 4.9990 chunk 565 optimal weight: 0.8980 chunk 596 optimal weight: 20.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN B 375 ASN C 120 GLN C 203 GLN C 441 GLN ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 ASN F 377 ASN ** L 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 54296 Z= 0.287 Angle : 0.632 16.428 73858 Z= 0.313 Chirality : 0.045 0.318 8366 Planarity : 0.005 0.061 9280 Dihedral : 10.639 179.957 7593 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.12 % Rotamer: Outliers : 0.60 % Allowed : 10.96 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -0.52 (0.10), residues: 6688 helix: 1.57 (0.13), residues: 1909 sheet: 0.70 (0.15), residues: 1212 loop : -1.93 (0.09), residues: 3567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 360 time to evaluate : 4.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 24 residues processed: 383 average time/residue: 1.4487 time to fit residues: 697.0751 Evaluate side-chains 376 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 352 time to evaluate : 4.572 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 7 average time/residue: 0.6399 time to fit residues: 13.0987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 392 optimal weight: 3.9990 chunk 632 optimal weight: 2.9990 chunk 386 optimal weight: 0.0030 chunk 300 optimal weight: 0.9980 chunk 439 optimal weight: 0.8980 chunk 663 optimal weight: 1.9990 chunk 610 optimal weight: 2.9990 chunk 528 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 408 optimal weight: 5.9990 chunk 323 optimal weight: 1.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN C 203 GLN C 441 GLN ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 ASN F 377 ASN ** L 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 54296 Z= 0.188 Angle : 0.593 15.779 73858 Z= 0.290 Chirality : 0.043 0.284 8366 Planarity : 0.005 0.061 9280 Dihedral : 10.445 179.730 7593 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 0.49 % Allowed : 11.06 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -0.45 (0.10), residues: 6688 helix: 1.57 (0.13), residues: 1921 sheet: 0.73 (0.14), residues: 1252 loop : -1.87 (0.10), residues: 3515 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 358 time to evaluate : 5.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 378 average time/residue: 1.4607 time to fit residues: 695.7826 Evaluate side-chains 373 residues out of total 5776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 353 time to evaluate : 4.647 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 5 average time/residue: 0.8407 time to fit residues: 13.4257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 419 optimal weight: 0.2980 chunk 562 optimal weight: 10.0000 chunk 161 optimal weight: 0.0980 chunk 487 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 529 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 543 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN C 364 GLN C 441 GLN D 389 GLN E 375 ASN F 377 ASN G 377 ASN ** L 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 442 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.113897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.070275 restraints weight = 240993.280| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 4.72 r_work: 0.2657 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 54296 Z= 0.150 Angle : 0.568 15.296 73858 Z= 0.274 Chirality : 0.042 0.265 8366 Planarity : 0.005 0.061 9280 Dihedral : 10.138 178.712 7593 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 0.47 % Allowed : 11.10 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -0.35 (0.10), residues: 6688 helix: 1.61 (0.13), residues: 1930 sheet: 0.79 (0.14), residues: 1292 loop : -1.83 (0.10), residues: 3466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13527.35 seconds wall clock time: 237 minutes 21.64 seconds (14241.64 seconds total)