Starting phenix.real_space_refine on Mon Feb 19 13:55:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqh_35670/02_2024/8iqh_35670.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqh_35670/02_2024/8iqh_35670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqh_35670/02_2024/8iqh_35670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqh_35670/02_2024/8iqh_35670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqh_35670/02_2024/8iqh_35670.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqh_35670/02_2024/8iqh_35670.pdb" } resolution = 3.67 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 283 5.16 5 C 50832 2.51 5 N 13697 2.21 5 O 14668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A ARG 624": "NH1" <-> "NH2" Residue "A ARG 647": "NH1" <-> "NH2" Residue "A ARG 686": "NH1" <-> "NH2" Residue "A ARG 704": "NH1" <-> "NH2" Residue "A ARG 751": "NH1" <-> "NH2" Residue "A ARG 754": "NH1" <-> "NH2" Residue "A ARG 757": "NH1" <-> "NH2" Residue "A ARG 779": "NH1" <-> "NH2" Residue "A ARG 829": "NH1" <-> "NH2" Residue "A ARG 837": "NH1" <-> "NH2" Residue "A ARG 842": "NH1" <-> "NH2" Residue "A ARG 907": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 267": "NH1" <-> "NH2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ARG 461": "NH1" <-> "NH2" Residue "B ARG 479": "NH1" <-> "NH2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B ARG 513": "NH1" <-> "NH2" Residue "B ARG 529": "NH1" <-> "NH2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B ARG 538": "NH1" <-> "NH2" Residue "B ARG 624": "NH1" <-> "NH2" Residue "B ARG 647": "NH1" <-> "NH2" Residue "B ARG 686": "NH1" <-> "NH2" Residue "B ARG 704": "NH1" <-> "NH2" Residue "B ARG 752": "NH1" <-> "NH2" Residue "B ARG 754": "NH1" <-> "NH2" Residue "B ARG 757": "NH1" <-> "NH2" Residue "B ARG 779": "NH1" <-> "NH2" Residue "B ARG 829": "NH1" <-> "NH2" Residue "B ARG 837": "NH1" <-> "NH2" Residue "B ARG 907": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 376": "NH1" <-> "NH2" Residue "C ARG 461": "NH1" <-> "NH2" Residue "C ARG 479": "NH1" <-> "NH2" Residue "C ARG 483": "NH1" <-> "NH2" Residue "C ARG 513": "NH1" <-> "NH2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C ARG 536": "NH1" <-> "NH2" Residue "C ARG 538": "NH1" <-> "NH2" Residue "C ARG 624": "NH1" <-> "NH2" Residue "C ARG 647": "NH1" <-> "NH2" Residue "C ARG 686": "NH1" <-> "NH2" Residue "C ARG 704": "NH1" <-> "NH2" Residue "C ARG 751": "NH1" <-> "NH2" Residue "C ARG 754": "NH1" <-> "NH2" Residue "C ARG 757": "NH1" <-> "NH2" Residue "C ARG 829": "NH1" <-> "NH2" Residue "C ARG 842": "NH1" <-> "NH2" Residue "C ARG 901": "NH1" <-> "NH2" Residue "C ARG 907": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 219": "NH1" <-> "NH2" Residue "D TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 267": "NH1" <-> "NH2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 376": "NH1" <-> "NH2" Residue "D ARG 461": "NH1" <-> "NH2" Residue "D ARG 479": "NH1" <-> "NH2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D ARG 513": "NH1" <-> "NH2" Residue "D ARG 529": "NH1" <-> "NH2" Residue "D ARG 536": "NH1" <-> "NH2" Residue "D ARG 538": "NH1" <-> "NH2" Residue "D ARG 611": "NH1" <-> "NH2" Residue "D ARG 624": "NH1" <-> "NH2" Residue "D ARG 682": "NH1" <-> "NH2" Residue "D ARG 686": "NH1" <-> "NH2" Residue "D ARG 704": "NH1" <-> "NH2" Residue "D ARG 751": "NH1" <-> "NH2" Residue "D ARG 752": "NH1" <-> "NH2" Residue "D ARG 757": "NH1" <-> "NH2" Residue "D ARG 829": "NH1" <-> "NH2" Residue "D ARG 837": "NH1" <-> "NH2" Residue "D ARG 874": "NH1" <-> "NH2" Residue "D ARG 901": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 33": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 219": "NH1" <-> "NH2" Residue "E ARG 267": "NH1" <-> "NH2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E ARG 461": "NH1" <-> "NH2" Residue "E ARG 479": "NH1" <-> "NH2" Residue "E ARG 483": "NH1" <-> "NH2" Residue "E ARG 513": "NH1" <-> "NH2" Residue "E ARG 529": "NH1" <-> "NH2" Residue "E ARG 536": "NH1" <-> "NH2" Residue "E ARG 538": "NH1" <-> "NH2" Residue "E ARG 624": "NH1" <-> "NH2" Residue "E ARG 647": "NH1" <-> "NH2" Residue "E ARG 686": "NH1" <-> "NH2" Residue "E ARG 704": "NH1" <-> "NH2" Residue "E ARG 751": "NH1" <-> "NH2" Residue "E ARG 752": "NH1" <-> "NH2" Residue "E ARG 754": "NH1" <-> "NH2" Residue "E ARG 757": "NH1" <-> "NH2" Residue "E ARG 837": "NH1" <-> "NH2" Residue "E ARG 842": "NH1" <-> "NH2" Residue "E ARG 901": "NH1" <-> "NH2" Residue "E ARG 907": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 33": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "F ARG 117": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 336": "NH1" <-> "NH2" Residue "F ARG 376": "NH1" <-> "NH2" Residue "F ARG 461": "NH1" <-> "NH2" Residue "F GLU 475": "OE1" <-> "OE2" Residue "F ARG 479": "NH1" <-> "NH2" Residue "F ARG 483": "NH1" <-> "NH2" Residue "F ARG 513": "NH1" <-> "NH2" Residue "F ARG 529": "NH1" <-> "NH2" Residue "F ARG 536": "NH1" <-> "NH2" Residue "F ARG 538": "NH1" <-> "NH2" Residue "F ARG 611": "NH1" <-> "NH2" Residue "F ARG 624": "NH1" <-> "NH2" Residue "F ARG 647": "NH1" <-> "NH2" Residue "F ARG 682": "NH1" <-> "NH2" Residue "F ARG 686": "NH1" <-> "NH2" Residue "F ARG 704": "NH1" <-> "NH2" Residue "F ARG 754": "NH1" <-> "NH2" Residue "F ARG 829": "NH1" <-> "NH2" Residue "F ARG 837": "NH1" <-> "NH2" Residue "F ARG 842": "NH1" <-> "NH2" Residue "F ARG 907": "NH1" <-> "NH2" Residue "G ARG 18": "NH1" <-> "NH2" Residue "G ARG 33": "NH1" <-> "NH2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G ARG 87": "NH1" <-> "NH2" Residue "G ARG 117": "NH1" <-> "NH2" Residue "G ARG 219": "NH1" <-> "NH2" Residue "G ARG 267": "NH1" <-> "NH2" Residue "G ARG 301": "NH1" <-> "NH2" Residue "G ARG 336": "NH1" <-> "NH2" Residue "G ARG 461": "NH1" <-> "NH2" Residue "G ARG 479": "NH1" <-> "NH2" Residue "G ARG 483": "NH1" <-> "NH2" Residue "G ARG 536": "NH1" <-> "NH2" Residue "G ARG 538": "NH1" <-> "NH2" Residue "G ARG 624": "NH1" <-> "NH2" Residue "G ARG 647": "NH1" <-> "NH2" Residue "G ARG 682": "NH1" <-> "NH2" Residue "G ARG 686": "NH1" <-> "NH2" Residue "G ARG 704": "NH1" <-> "NH2" Residue "G ARG 751": "NH1" <-> "NH2" Residue "G ARG 752": "NH1" <-> "NH2" Residue "G ARG 754": "NH1" <-> "NH2" Residue "G ARG 829": "NH1" <-> "NH2" Residue "G ARG 874": "NH1" <-> "NH2" Residue "G ARG 901": "NH1" <-> "NH2" Residue "G ARG 907": "NH1" <-> "NH2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H ARG 52": "NH1" <-> "NH2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H ARG 121": "NH1" <-> "NH2" Residue "H ARG 219": "NH1" <-> "NH2" Residue "H ARG 267": "NH1" <-> "NH2" Residue "H ARG 336": "NH1" <-> "NH2" Residue "H ARG 461": "NH1" <-> "NH2" Residue "H ARG 479": "NH1" <-> "NH2" Residue "H ARG 483": "NH1" <-> "NH2" Residue "H ARG 513": "NH1" <-> "NH2" Residue "H ARG 529": "NH1" <-> "NH2" Residue "H GLU 532": "OE1" <-> "OE2" Residue "H ARG 536": "NH1" <-> "NH2" Residue "H ARG 538": "NH1" <-> "NH2" Residue "H ARG 647": "NH1" <-> "NH2" Residue "H ARG 682": "NH1" <-> "NH2" Residue "H ARG 704": "NH1" <-> "NH2" Residue "H ARG 751": "NH1" <-> "NH2" Residue "H ARG 754": "NH1" <-> "NH2" Residue "H ARG 757": "NH1" <-> "NH2" Residue "H ARG 829": "NH1" <-> "NH2" Residue "H ARG 837": "NH1" <-> "NH2" Residue "H ARG 842": "NH1" <-> "NH2" Residue "H ARG 874": "NH1" <-> "NH2" Residue "H ARG 901": "NH1" <-> "NH2" Residue "H ARG 907": "NH1" <-> "NH2" Residue "I ARG 67": "NH1" <-> "NH2" Residue "I ARG 76": "NH1" <-> "NH2" Residue "I ARG 87": "NH1" <-> "NH2" Residue "I ARG 219": "NH1" <-> "NH2" Residue "I ARG 267": "NH1" <-> "NH2" Residue "I GLU 317": "OE1" <-> "OE2" Residue "I ARG 376": "NH1" <-> "NH2" Residue "I ARG 461": "NH1" <-> "NH2" Residue "I ARG 479": "NH1" <-> "NH2" Residue "I ARG 483": "NH1" <-> "NH2" Residue "I ARG 513": "NH1" <-> "NH2" Residue "I ARG 529": "NH1" <-> "NH2" Residue "I ARG 536": "NH1" <-> "NH2" Residue "I ARG 538": "NH1" <-> "NH2" Residue "J ARG 33": "NH1" <-> "NH2" Residue "J ARG 52": "NH1" <-> "NH2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 76": "NH1" <-> "NH2" Residue "J ARG 87": "NH1" <-> "NH2" Residue "J ARG 117": "NH1" <-> "NH2" Residue "J ARG 121": "NH1" <-> "NH2" Residue "J ARG 219": "NH1" <-> "NH2" Residue "J ARG 267": "NH1" <-> "NH2" Residue "J ARG 301": "NH1" <-> "NH2" Residue "J ARG 376": "NH1" <-> "NH2" Residue "J ARG 461": "NH1" <-> "NH2" Residue "J ARG 483": "NH1" <-> "NH2" Residue "J ARG 513": "NH1" <-> "NH2" Residue "J ARG 529": "NH1" <-> "NH2" Residue "J ARG 536": "NH1" <-> "NH2" Residue "J ARG 538": "NH1" <-> "NH2" Residue "K ARG 33": "NH1" <-> "NH2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "K ARG 67": "NH1" <-> "NH2" Residue "K ARG 76": "NH1" <-> "NH2" Residue "K ARG 87": "NH1" <-> "NH2" Residue "K ARG 121": "NH1" <-> "NH2" Residue "K ARG 267": "NH1" <-> "NH2" Residue "K ARG 301": "NH1" <-> "NH2" Residue "K ARG 336": "NH1" <-> "NH2" Residue "K ARG 376": "NH1" <-> "NH2" Residue "K ARG 461": "NH1" <-> "NH2" Residue "K ARG 513": "NH1" <-> "NH2" Residue "K ARG 536": "NH1" <-> "NH2" Residue "K ARG 538": "NH1" <-> "NH2" Residue "K ARG 611": "NH1" <-> "NH2" Residue "K ARG 647": "NH1" <-> "NH2" Residue "K ARG 751": "NH1" <-> "NH2" Residue "K ARG 752": "NH1" <-> "NH2" Residue "K ARG 754": "NH1" <-> "NH2" Residue "K ARG 757": "NH1" <-> "NH2" Residue "K ARG 829": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 52": "NH1" <-> "NH2" Residue "M ARG 67": "NH1" <-> "NH2" Residue "M ARG 76": "NH1" <-> "NH2" Residue "M ARG 87": "NH1" <-> "NH2" Residue "M ARG 121": "NH1" <-> "NH2" Residue "M ARG 301": "NH1" <-> "NH2" Residue "M ARG 336": "NH1" <-> "NH2" Residue "M ARG 376": "NH1" <-> "NH2" Residue "M ARG 461": "NH1" <-> "NH2" Residue "M ARG 479": "NH1" <-> "NH2" Residue "M ARG 483": "NH1" <-> "NH2" Residue "M ARG 513": "NH1" <-> "NH2" Residue "M ARG 529": "NH1" <-> "NH2" Residue "M ARG 536": "NH1" <-> "NH2" Residue "M ARG 538": "NH1" <-> "NH2" Residue "M ARG 611": "NH1" <-> "NH2" Residue "M ARG 624": "NH1" <-> "NH2" Residue "M ARG 647": "NH1" <-> "NH2" Residue "M ARG 686": "NH1" <-> "NH2" Residue "M ARG 754": "NH1" <-> "NH2" Residue "M ARG 757": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 79480 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 882, 6950 Classifications: {'peptide': 882} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 84} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 840} Chain breaks: 7 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Chain: "B" Number of atoms: 6975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 892, 6975 Classifications: {'peptide': 892} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 849} Chain breaks: 5 Unresolved non-hydrogen bonds: 368 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 297 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 165 Chain: "C" Number of atoms: 7010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 7010 Classifications: {'peptide': 891} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 848} Chain breaks: 5 Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 407 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 171 Chain: "D" Number of atoms: 6864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 6864 Classifications: {'peptide': 891} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 848} Chain breaks: 5 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 227 Chain: "E" Number of atoms: 6874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 6874 Classifications: {'peptide': 880} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 840} Chain breaks: 7 Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 495 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 216 Chain: "F" Number of atoms: 6789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 6789 Classifications: {'peptide': 880} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 839} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 600 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 250 Chain: "G" Number of atoms: 6656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 863, 6656 Classifications: {'peptide': 863} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 823} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 581 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 233 Chain: "H" Number of atoms: 6684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 6684 Classifications: {'peptide': 872} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 829} Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 524 Unresolved non-hydrogen angles: 664 Unresolved non-hydrogen dihedrals: 455 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 10, 'TRP:plan': 4, 'HIS:plan': 6, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 295 Chain: "I" Number of atoms: 5967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 866, 5967 Classifications: {'peptide': 866} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 300} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 823} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1222 Unresolved non-hydrogen angles: 1561 Unresolved non-hydrogen dihedrals: 1039 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 8, 'TYR:plan': 18, 'ASN:plan1': 23, 'TRP:plan': 7, 'HIS:plan': 11, 'PHE:plan': 15, 'GLU:plan': 35, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 741 Chain: "J" Number of atoms: 6003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6003 Classifications: {'peptide': 881} Incomplete info: {'truncation_to_alanine': 341} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 838} Chain breaks: 6 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1316 Unresolved non-hydrogen angles: 1689 Unresolved non-hydrogen dihedrals: 1127 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 8, 'TYR:plan': 17, 'ASN:plan1': 27, 'TRP:plan': 10, 'ASP:plan': 10, 'PHE:plan': 16, 'GLU:plan': 32, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 732 Chain: "K" Number of atoms: 6312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 866, 6312 Classifications: {'peptide': 866} Incomplete info: {'truncation_to_alanine': 224} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 823} Chain breaks: 8 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 861 Unresolved non-hydrogen angles: 1100 Unresolved non-hydrogen dihedrals: 730 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 7, 'TYR:plan': 10, 'ASN:plan1': 16, 'TRP:plan': 6, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 22, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 473 Chain: "M" Number of atoms: 6396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 871, 6396 Classifications: {'peptide': 871} Incomplete info: {'truncation_to_alanine': 211} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 831} Chain breaks: 9 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 810 Unresolved non-hydrogen angles: 1033 Unresolved non-hydrogen dihedrals: 685 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 5, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 6, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 419 Time building chain proxies: 30.42, per 1000 atoms: 0.38 Number of scatterers: 79480 At special positions: 0 Unit cell: (284.9, 286, 192.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 283 16.00 O 14668 8.00 N 13697 7.00 C 50832 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: 23.59 Conformation dependent library (CDL) restraints added in 10.8 seconds 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20164 Finding SS restraints... Secondary structure from input PDB file: 495 helices and 113 sheets defined 53.2% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.76 Creating SS restraints... Processing helix chain 'A' and resid 10 through 18 removed outlier: 3.870A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 34 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 61 through 78 removed outlier: 4.039A pdb=" N ARG A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN A 78 " --> pdb=" O GLN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 130 Processing helix chain 'A' and resid 149 through 153 removed outlier: 4.055A pdb=" N GLY A 152 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 180 through 189 removed outlier: 3.780A pdb=" N GLU A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.530A pdb=" N CYS A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 4.331A pdb=" N ALA A 204 " --> pdb=" O PRO A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 250 removed outlier: 4.008A pdb=" N TYR A 250 " --> pdb=" O ILE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 288 through 297 Processing helix chain 'A' and resid 297 through 308 removed outlier: 3.852A pdb=" N ASN A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 310 No H-bonds generated for 'chain 'A' and resid 309 through 310' Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.590A pdb=" N VAL A 316 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.546A pdb=" N THR A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.918A pdb=" N ILE A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 409 removed outlier: 3.520A pdb=" N TYR A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 removed outlier: 3.515A pdb=" N ILE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 494 removed outlier: 3.874A pdb=" N SER A 474 " --> pdb=" O HIS A 470 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE A 477 " --> pdb=" O ILE A 473 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 516 removed outlier: 4.017A pdb=" N SER A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 520 through 535 removed outlier: 4.353A pdb=" N PHE A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU A 534 " --> pdb=" O GLN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 544 Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 607 through 619 Processing helix chain 'A' and resid 641 through 657 removed outlier: 5.825A pdb=" N ASP A 655 " --> pdb=" O MET A 651 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N HIS A 656 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.648A pdb=" N THR A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 701 through 709 Processing helix chain 'A' and resid 746 through 752 removed outlier: 3.810A pdb=" N ARG A 752 " --> pdb=" O GLY A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 783 removed outlier: 3.797A pdb=" N HIS A 782 " --> pdb=" O PRO A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 786 No H-bonds generated for 'chain 'A' and resid 784 through 786' Processing helix chain 'A' and resid 787 through 810 Processing helix chain 'A' and resid 818 through 833 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 855 through 870 Processing helix chain 'A' and resid 879 through 886 removed outlier: 3.752A pdb=" N ASN A 886 " --> pdb=" O GLN A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.238A pdb=" N LYS A 891 " --> pdb=" O VAL A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 945 Processing helix chain 'B' and resid 11 through 21 Processing helix chain 'B' and resid 21 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 61 through 77 removed outlier: 3.942A pdb=" N ARG B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 130 Processing helix chain 'B' and resid 166 through 178 Processing helix chain 'B' and resid 180 through 189 removed outlier: 4.331A pdb=" N GLU B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 removed outlier: 3.849A pdb=" N ALA B 204 " --> pdb=" O PRO B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 297 through 308 removed outlier: 3.824A pdb=" N ASN B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 310 No H-bonds generated for 'chain 'B' and resid 309 through 310' Processing helix chain 'B' and resid 311 through 315 Processing helix chain 'B' and resid 317 through 332 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 353 through 368 Processing helix chain 'B' and resid 374 through 386 removed outlier: 3.865A pdb=" N ILE B 378 " --> pdb=" O THR B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 409 removed outlier: 3.619A pdb=" N TYR B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 427 Processing helix chain 'B' and resid 466 through 494 removed outlier: 3.699A pdb=" N SER B 474 " --> pdb=" O HIS B 470 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE B 477 " --> pdb=" O ILE B 473 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG B 479 " --> pdb=" O GLU B 475 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 514 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.755A pdb=" N ILE B 518 " --> pdb=" O LYS B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 535 removed outlier: 4.286A pdb=" N PHE B 533 " --> pdb=" O ARG B 529 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 544 Processing helix chain 'B' and resid 591 through 605 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.508A pdb=" N THR B 620 " --> pdb=" O PHE B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 641 through 657 removed outlier: 5.944A pdb=" N ASP B 655 " --> pdb=" O MET B 651 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N HIS B 656 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 668 removed outlier: 3.588A pdb=" N THR B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 684 Processing helix chain 'B' and resid 701 through 709 Processing helix chain 'B' and resid 746 through 752 removed outlier: 3.620A pdb=" N ARG B 752 " --> pdb=" O GLY B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 783 removed outlier: 4.092A pdb=" N HIS B 782 " --> pdb=" O PRO B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 810 Processing helix chain 'B' and resid 812 through 816 Processing helix chain 'B' and resid 818 through 833 Processing helix chain 'B' and resid 833 through 842 Processing helix chain 'B' and resid 855 through 870 Processing helix chain 'B' and resid 876 through 886 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.628A pdb=" N LYS B 891 " --> pdb=" O VAL B 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 21 Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 61 through 78 removed outlier: 3.889A pdb=" N ARG C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN C 78 " --> pdb=" O GLN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 167 through 178 Processing helix chain 'C' and resid 180 through 189 removed outlier: 4.047A pdb=" N GLU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 198 removed outlier: 3.517A pdb=" N SER C 197 " --> pdb=" O ASN C 194 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS C 198 " --> pdb=" O PRO C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 198' Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 297 through 308 Processing helix chain 'C' and resid 309 through 310 No H-bonds generated for 'chain 'C' and resid 309 through 310' Processing helix chain 'C' and resid 311 through 316 removed outlier: 3.644A pdb=" N VAL C 316 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 332 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 353 through 368 Processing helix chain 'C' and resid 374 through 386 removed outlier: 3.920A pdb=" N ILE C 378 " --> pdb=" O THR C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 409 removed outlier: 3.661A pdb=" N TYR C 409 " --> pdb=" O TYR C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 426 Processing helix chain 'C' and resid 466 through 476 removed outlier: 3.819A pdb=" N SER C 474 " --> pdb=" O HIS C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 494 removed outlier: 3.865A pdb=" N VAL C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 516 removed outlier: 4.128A pdb=" N SER C 516 " --> pdb=" O GLU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 519 No H-bonds generated for 'chain 'C' and resid 517 through 519' Processing helix chain 'C' and resid 520 through 535 removed outlier: 4.520A pdb=" N PHE C 533 " --> pdb=" O ARG C 529 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 544 Processing helix chain 'C' and resid 591 through 605 Processing helix chain 'C' and resid 607 through 619 Processing helix chain 'C' and resid 620 through 623 Processing helix chain 'C' and resid 641 through 654 Processing helix chain 'C' and resid 663 through 668 Processing helix chain 'C' and resid 679 through 684 removed outlier: 3.777A pdb=" N LEU C 683 " --> pdb=" O PHE C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 710 Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.827A pdb=" N ARG C 752 " --> pdb=" O GLY C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 781 Processing helix chain 'C' and resid 787 through 810 Processing helix chain 'C' and resid 818 through 833 Processing helix chain 'C' and resid 833 through 842 Processing helix chain 'C' and resid 855 through 870 Processing helix chain 'C' and resid 876 through 886 removed outlier: 3.832A pdb=" N ASN C 886 " --> pdb=" O GLN C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.147A pdb=" N LYS C 891 " --> pdb=" O VAL C 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 21 removed outlier: 3.536A pdb=" N ARG D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS D 19 " --> pdb=" O THR D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 34 Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 61 through 78 removed outlier: 4.001A pdb=" N ARG D 67 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN D 78 " --> pdb=" O GLN D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 130 Processing helix chain 'D' and resid 166 through 179 removed outlier: 3.945A pdb=" N HIS D 179 " --> pdb=" O ALA D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 189 removed outlier: 3.614A pdb=" N GLN D 184 " --> pdb=" O ASP D 180 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 205 removed outlier: 4.210A pdb=" N ALA D 204 " --> pdb=" O PRO D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 287 through 297 Processing helix chain 'D' and resid 297 through 308 removed outlier: 3.554A pdb=" N ASN D 308 " --> pdb=" O HIS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 312 through 317 removed outlier: 3.792A pdb=" N VAL D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 332 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.767A pdb=" N THR D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 368 Processing helix chain 'D' and resid 374 through 386 removed outlier: 3.904A pdb=" N ILE D 378 " --> pdb=" O THR D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 409 removed outlier: 3.657A pdb=" N TYR D 409 " --> pdb=" O TYR D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 427 removed outlier: 3.523A pdb=" N ILE D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 476 Processing helix chain 'D' and resid 476 through 494 removed outlier: 3.968A pdb=" N VAL D 480 " --> pdb=" O ASN D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 516 removed outlier: 4.231A pdb=" N SER D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 519 No H-bonds generated for 'chain 'D' and resid 517 through 519' Processing helix chain 'D' and resid 520 through 535 removed outlier: 4.341A pdb=" N PHE D 533 " --> pdb=" O ARG D 529 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU D 534 " --> pdb=" O GLN D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 544 Processing helix chain 'D' and resid 591 through 605 Processing helix chain 'D' and resid 607 through 620 Processing helix chain 'D' and resid 621 through 623 No H-bonds generated for 'chain 'D' and resid 621 through 623' Processing helix chain 'D' and resid 641 through 654 Processing helix chain 'D' and resid 663 through 668 Processing helix chain 'D' and resid 679 through 684 removed outlier: 3.940A pdb=" N LEU D 683 " --> pdb=" O PHE D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 709 Processing helix chain 'D' and resid 746 through 752 removed outlier: 3.970A pdb=" N ARG D 752 " --> pdb=" O GLY D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 783 removed outlier: 4.214A pdb=" N HIS D 782 " --> pdb=" O PRO D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 810 Processing helix chain 'D' and resid 818 through 833 Processing helix chain 'D' and resid 833 through 842 Processing helix chain 'D' and resid 854 through 870 Processing helix chain 'D' and resid 876 through 887 Processing helix chain 'D' and resid 888 through 891 removed outlier: 3.889A pdb=" N LYS D 891 " --> pdb=" O VAL D 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 888 through 891' Processing helix chain 'E' and resid 11 through 20 Processing helix chain 'E' and resid 21 through 34 Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 61 through 78 removed outlier: 4.183A pdb=" N ARG E 67 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN E 78 " --> pdb=" O GLN E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 130 Processing helix chain 'E' and resid 149 through 151 No H-bonds generated for 'chain 'E' and resid 149 through 151' Processing helix chain 'E' and resid 166 through 179 removed outlier: 3.693A pdb=" N HIS E 179 " --> pdb=" O ALA E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 189 removed outlier: 3.759A pdb=" N GLU E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 250 Processing helix chain 'E' and resid 251 through 257 Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 297 through 308 removed outlier: 3.661A pdb=" N ASN E 308 " --> pdb=" O HIS E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 310 No H-bonds generated for 'chain 'E' and resid 309 through 310' Processing helix chain 'E' and resid 311 through 315 Processing helix chain 'E' and resid 317 through 332 Processing helix chain 'E' and resid 335 through 344 removed outlier: 3.603A pdb=" N SER E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 353 through 366 removed outlier: 3.574A pdb=" N LYS E 357 " --> pdb=" O GLY E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 386 removed outlier: 3.786A pdb=" N ILE E 378 " --> pdb=" O THR E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 409 Processing helix chain 'E' and resid 414 through 426 removed outlier: 3.507A pdb=" N ILE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 476 removed outlier: 3.651A pdb=" N SER E 474 " --> pdb=" O HIS E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 494 removed outlier: 3.907A pdb=" N VAL E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 516 removed outlier: 4.105A pdb=" N SER E 516 " --> pdb=" O GLU E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 519 No H-bonds generated for 'chain 'E' and resid 517 through 519' Processing helix chain 'E' and resid 520 through 535 removed outlier: 4.286A pdb=" N PHE E 533 " --> pdb=" O ARG E 529 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU E 534 " --> pdb=" O GLN E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 544 Processing helix chain 'E' and resid 591 through 605 Processing helix chain 'E' and resid 607 through 619 Processing helix chain 'E' and resid 641 through 657 removed outlier: 5.883A pdb=" N ASP E 655 " --> pdb=" O MET E 651 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N HIS E 656 " --> pdb=" O VAL E 652 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR E 657 " --> pdb=" O LEU E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 663 through 668 Processing helix chain 'E' and resid 680 through 684 removed outlier: 3.561A pdb=" N LEU E 683 " --> pdb=" O PHE E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 710 Processing helix chain 'E' and resid 746 through 752 removed outlier: 4.303A pdb=" N ARG E 752 " --> pdb=" O GLY E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 778 through 783 removed outlier: 3.855A pdb=" N HIS E 782 " --> pdb=" O PRO E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 810 Processing helix chain 'E' and resid 812 through 816 Processing helix chain 'E' and resid 818 through 833 Processing helix chain 'E' and resid 833 through 842 Processing helix chain 'E' and resid 855 through 870 Processing helix chain 'E' and resid 881 through 886 Processing helix chain 'E' and resid 887 through 891 removed outlier: 3.697A pdb=" N LYS E 891 " --> pdb=" O VAL E 888 " (cutoff:3.500A) Processing helix chain 'E' and resid 941 through 945 Processing helix chain 'F' and resid 11 through 21 Processing helix chain 'F' and resid 21 through 34 Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 61 through 78 removed outlier: 4.172A pdb=" N ARG F 67 " --> pdb=" O THR F 63 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN F 78 " --> pdb=" O GLN F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 130 Processing helix chain 'F' and resid 166 through 178 Processing helix chain 'F' and resid 180 through 189 removed outlier: 3.759A pdb=" N GLU F 189 " --> pdb=" O LYS F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 199 removed outlier: 4.258A pdb=" N LEU F 199 " --> pdb=" O GLU F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 205 removed outlier: 4.153A pdb=" N ALA F 204 " --> pdb=" O PRO F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 250 Processing helix chain 'F' and resid 251 through 257 Processing helix chain 'F' and resid 287 through 297 Processing helix chain 'F' and resid 297 through 308 removed outlier: 3.839A pdb=" N ASN F 308 " --> pdb=" O HIS F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 310 No H-bonds generated for 'chain 'F' and resid 309 through 310' Processing helix chain 'F' and resid 311 through 316 removed outlier: 3.598A pdb=" N VAL F 316 " --> pdb=" O GLU F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 332 removed outlier: 3.584A pdb=" N SER F 332 " --> pdb=" O LEU F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 344 Processing helix chain 'F' and resid 346 through 352 removed outlier: 3.643A pdb=" N TRP F 350 " --> pdb=" O CYS F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 367 Processing helix chain 'F' and resid 374 through 386 removed outlier: 3.899A pdb=" N ILE F 378 " --> pdb=" O THR F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 409 Processing helix chain 'F' and resid 414 through 426 removed outlier: 3.532A pdb=" N ILE F 418 " --> pdb=" O GLU F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 476 removed outlier: 3.802A pdb=" N SER F 474 " --> pdb=" O HIS F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 494 removed outlier: 3.954A pdb=" N VAL F 480 " --> pdb=" O ASN F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 516 removed outlier: 4.171A pdb=" N SER F 516 " --> pdb=" O GLU F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 519 No H-bonds generated for 'chain 'F' and resid 517 through 519' Processing helix chain 'F' and resid 520 through 535 removed outlier: 4.136A pdb=" N PHE F 533 " --> pdb=" O ARG F 529 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU F 534 " --> pdb=" O GLN F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 544 Processing helix chain 'F' and resid 591 through 605 Processing helix chain 'F' and resid 607 through 619 Processing helix chain 'F' and resid 620 through 623 Processing helix chain 'F' and resid 641 through 654 Processing helix chain 'F' and resid 662 through 668 removed outlier: 4.272A pdb=" N LEU F 666 " --> pdb=" O ASN F 662 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER F 668 " --> pdb=" O SER F 664 " (cutoff:3.500A) Processing helix chain 'F' and resid 680 through 684 removed outlier: 3.771A pdb=" N LEU F 683 " --> pdb=" O PHE F 680 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 709 Processing helix chain 'F' and resid 746 through 752 removed outlier: 3.817A pdb=" N ARG F 752 " --> pdb=" O GLY F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 777 through 783 removed outlier: 4.258A pdb=" N ILE F 781 " --> pdb=" O ASP F 777 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N HIS F 782 " --> pdb=" O PRO F 778 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 810 Processing helix chain 'F' and resid 818 through 833 Processing helix chain 'F' and resid 833 through 842 Processing helix chain 'F' and resid 855 through 870 Processing helix chain 'F' and resid 879 through 886 Processing helix chain 'F' and resid 887 through 891 removed outlier: 3.935A pdb=" N LYS F 891 " --> pdb=" O VAL F 888 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 18 Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'G' and resid 61 through 77 removed outlier: 3.820A pdb=" N ARG G 67 " --> pdb=" O THR G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 167 through 178 Processing helix chain 'G' and resid 180 through 190 removed outlier: 3.564A pdb=" N GLU G 189 " --> pdb=" O LYS G 185 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN G 190 " --> pdb=" O ILE G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 198 Processing helix chain 'G' and resid 200 through 205 removed outlier: 4.315A pdb=" N ALA G 204 " --> pdb=" O PRO G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 257 Processing helix chain 'G' and resid 288 through 297 Processing helix chain 'G' and resid 297 through 308 removed outlier: 3.623A pdb=" N ASN G 308 " --> pdb=" O HIS G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 311 No H-bonds generated for 'chain 'G' and resid 309 through 311' Processing helix chain 'G' and resid 312 through 317 removed outlier: 3.879A pdb=" N VAL G 316 " --> pdb=" O PRO G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 332 Processing helix chain 'G' and resid 335 through 344 Processing helix chain 'G' and resid 356 through 363 Processing helix chain 'G' and resid 374 through 386 removed outlier: 3.716A pdb=" N ILE G 378 " --> pdb=" O THR G 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 409 Processing helix chain 'G' and resid 414 through 427 removed outlier: 3.571A pdb=" N ILE G 418 " --> pdb=" O GLU G 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 466 through 494 removed outlier: 3.593A pdb=" N SER G 474 " --> pdb=" O HIS G 470 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE G 477 " --> pdb=" O ILE G 473 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER G 478 " --> pdb=" O SER G 474 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG G 479 " --> pdb=" O GLU G 475 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL G 480 " --> pdb=" O ASN G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 516 removed outlier: 3.918A pdb=" N SER G 516 " --> pdb=" O GLU G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 517 through 519 No H-bonds generated for 'chain 'G' and resid 517 through 519' Processing helix chain 'G' and resid 520 through 535 removed outlier: 4.448A pdb=" N PHE G 533 " --> pdb=" O ARG G 529 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU G 534 " --> pdb=" O GLN G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 591 through 605 Processing helix chain 'G' and resid 607 through 619 Processing helix chain 'G' and resid 620 through 623 Processing helix chain 'G' and resid 641 through 657 removed outlier: 5.776A pdb=" N ASP G 655 " --> pdb=" O MET G 651 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N HIS G 656 " --> pdb=" O VAL G 652 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR G 657 " --> pdb=" O LEU G 653 " (cutoff:3.500A) Processing helix chain 'G' and resid 663 through 668 Processing helix chain 'G' and resid 678 through 684 Processing helix chain 'G' and resid 701 through 709 Processing helix chain 'G' and resid 746 through 752 removed outlier: 3.942A pdb=" N ARG G 752 " --> pdb=" O GLY G 748 " (cutoff:3.500A) Processing helix chain 'G' and resid 787 through 810 Processing helix chain 'G' and resid 818 through 833 Processing helix chain 'G' and resid 833 through 842 removed outlier: 3.750A pdb=" N ARG G 837 " --> pdb=" O ASP G 833 " (cutoff:3.500A) Processing helix chain 'G' and resid 854 through 870 Processing helix chain 'G' and resid 876 through 886 removed outlier: 3.587A pdb=" N ASN G 886 " --> pdb=" O GLN G 882 " (cutoff:3.500A) Processing helix chain 'G' and resid 887 through 891 removed outlier: 3.947A pdb=" N LYS G 891 " --> pdb=" O VAL G 888 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 21 Processing helix chain 'H' and resid 21 through 34 Processing helix chain 'H' and resid 35 through 37 No H-bonds generated for 'chain 'H' and resid 35 through 37' Processing helix chain 'H' and resid 61 through 77 removed outlier: 4.437A pdb=" N ARG H 67 " --> pdb=" O THR H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 130 Processing helix chain 'H' and resid 167 through 178 Processing helix chain 'H' and resid 180 through 189 removed outlier: 3.831A pdb=" N GLU H 189 " --> pdb=" O LYS H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 205 removed outlier: 4.362A pdb=" N ALA H 204 " --> pdb=" O PRO H 201 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER H 205 " --> pdb=" O HIS H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 250 Processing helix chain 'H' and resid 251 through 257 Processing helix chain 'H' and resid 290 through 297 Processing helix chain 'H' and resid 297 through 308 removed outlier: 3.826A pdb=" N ASN H 308 " --> pdb=" O HIS H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 310 No H-bonds generated for 'chain 'H' and resid 309 through 310' Processing helix chain 'H' and resid 311 through 316 Processing helix chain 'H' and resid 317 through 332 Processing helix chain 'H' and resid 335 through 344 Processing helix chain 'H' and resid 346 through 351 Processing helix chain 'H' and resid 353 through 368 Processing helix chain 'H' and resid 374 through 386 removed outlier: 4.041A pdb=" N ILE H 378 " --> pdb=" O THR H 374 " (cutoff:3.500A) Processing helix chain 'H' and resid 386 through 409 removed outlier: 3.562A pdb=" N TYR H 409 " --> pdb=" O TYR H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 426 removed outlier: 3.548A pdb=" N ILE H 418 " --> pdb=" O GLU H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 466 through 476 removed outlier: 3.774A pdb=" N SER H 474 " --> pdb=" O HIS H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 494 removed outlier: 3.952A pdb=" N VAL H 480 " --> pdb=" O ASN H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 497 through 514 Processing helix chain 'H' and resid 515 through 519 removed outlier: 3.767A pdb=" N ILE H 518 " --> pdb=" O LYS H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 520 through 535 removed outlier: 4.335A pdb=" N PHE H 533 " --> pdb=" O ARG H 529 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU H 534 " --> pdb=" O GLN H 530 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 544 Processing helix chain 'H' and resid 591 through 605 Processing helix chain 'H' and resid 607 through 619 Processing helix chain 'H' and resid 620 through 623 Processing helix chain 'H' and resid 641 through 657 removed outlier: 6.010A pdb=" N ASP H 655 " --> pdb=" O MET H 651 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N HIS H 656 " --> pdb=" O VAL H 652 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR H 657 " --> pdb=" O LEU H 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 662 through 668 removed outlier: 4.242A pdb=" N LEU H 666 " --> pdb=" O ASN H 662 " (cutoff:3.500A) Processing helix chain 'H' and resid 680 through 684 Processing helix chain 'H' and resid 701 through 709 Processing helix chain 'H' and resid 746 through 752 removed outlier: 3.703A pdb=" N TRP H 750 " --> pdb=" O ASP H 746 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG H 752 " --> pdb=" O GLY H 748 " (cutoff:3.500A) Processing helix chain 'H' and resid 777 through 783 removed outlier: 4.297A pdb=" N ILE H 781 " --> pdb=" O ASP H 777 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS H 782 " --> pdb=" O PRO H 778 " (cutoff:3.500A) Processing helix chain 'H' and resid 787 through 810 Processing helix chain 'H' and resid 818 through 833 Processing helix chain 'H' and resid 833 through 842 Processing helix chain 'H' and resid 855 through 870 Processing helix chain 'H' and resid 876 through 886 Processing helix chain 'H' and resid 887 through 891 removed outlier: 3.836A pdb=" N LYS H 891 " --> pdb=" O VAL H 888 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 21 Processing helix chain 'I' and resid 21 through 34 Processing helix chain 'I' and resid 35 through 37 No H-bonds generated for 'chain 'I' and resid 35 through 37' Processing helix chain 'I' and resid 61 through 77 removed outlier: 4.231A pdb=" N ARG I 67 " --> pdb=" O THR I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 128 Processing helix chain 'I' and resid 166 through 179 removed outlier: 4.095A pdb=" N HIS I 179 " --> pdb=" O ALA I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 189 removed outlier: 3.658A pdb=" N GLN I 184 " --> pdb=" O ASP I 180 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU I 189 " --> pdb=" O LYS I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 205 removed outlier: 3.842A pdb=" N ALA I 204 " --> pdb=" O PRO I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 250 removed outlier: 3.598A pdb=" N TYR I 250 " --> pdb=" O ILE I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 256 Processing helix chain 'I' and resid 290 through 296 Processing helix chain 'I' and resid 297 through 308 removed outlier: 3.790A pdb=" N ASN I 308 " --> pdb=" O HIS I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 311 No H-bonds generated for 'chain 'I' and resid 309 through 311' Processing helix chain 'I' and resid 312 through 317 removed outlier: 3.910A pdb=" N VAL I 316 " --> pdb=" O PRO I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 332 Processing helix chain 'I' and resid 335 through 344 Processing helix chain 'I' and resid 346 through 352 removed outlier: 3.706A pdb=" N THR I 352 " --> pdb=" O GLU I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 353 through 367 Processing helix chain 'I' and resid 374 through 386 removed outlier: 3.752A pdb=" N ILE I 378 " --> pdb=" O THR I 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 386 through 409 removed outlier: 3.691A pdb=" N TYR I 409 " --> pdb=" O TYR I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 426 Processing helix chain 'I' and resid 466 through 494 removed outlier: 3.806A pdb=" N SER I 474 " --> pdb=" O HIS I 470 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE I 477 " --> pdb=" O ILE I 473 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER I 478 " --> pdb=" O SER I 474 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG I 479 " --> pdb=" O GLU I 475 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL I 480 " --> pdb=" O ASN I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 516 removed outlier: 4.140A pdb=" N SER I 516 " --> pdb=" O GLU I 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 517 through 519 No H-bonds generated for 'chain 'I' and resid 517 through 519' Processing helix chain 'I' and resid 520 through 535 removed outlier: 4.257A pdb=" N PHE I 533 " --> pdb=" O ARG I 529 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU I 534 " --> pdb=" O GLN I 530 " (cutoff:3.500A) Processing helix chain 'I' and resid 540 through 544 Processing helix chain 'I' and resid 591 through 605 Processing helix chain 'I' and resid 607 through 619 Processing helix chain 'I' and resid 641 through 653 removed outlier: 3.935A pdb=" N ALA I 650 " --> pdb=" O MET I 646 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU I 653 " --> pdb=" O VAL I 649 " (cutoff:3.500A) Processing helix chain 'I' and resid 679 through 684 Processing helix chain 'I' and resid 702 through 710 removed outlier: 4.278A pdb=" N LYS I 706 " --> pdb=" O SER I 703 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N MET I 708 " --> pdb=" O LEU I 705 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL I 709 " --> pdb=" O LYS I 706 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN I 710 " --> pdb=" O GLU I 707 " (cutoff:3.500A) Processing helix chain 'I' and resid 746 through 752 removed outlier: 4.042A pdb=" N ARG I 752 " --> pdb=" O GLY I 748 " (cutoff:3.500A) Processing helix chain 'I' and resid 778 through 783 removed outlier: 4.035A pdb=" N HIS I 782 " --> pdb=" O PRO I 778 " (cutoff:3.500A) Processing helix chain 'I' and resid 787 through 810 removed outlier: 3.684A pdb=" N GLN I 791 " --> pdb=" O ASP I 787 " (cutoff:3.500A) Processing helix chain 'I' and resid 812 through 816 Processing helix chain 'I' and resid 818 through 833 Processing helix chain 'I' and resid 833 through 842 Processing helix chain 'I' and resid 855 through 870 Processing helix chain 'I' and resid 876 through 886 removed outlier: 3.624A pdb=" N LEU I 880 " --> pdb=" O ILE I 876 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN I 882 " --> pdb=" O LEU I 878 " (cutoff:3.500A) Processing helix chain 'I' and resid 887 through 891 removed outlier: 4.281A pdb=" N LYS I 891 " --> pdb=" O VAL I 888 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 21 Processing helix chain 'J' and resid 21 through 34 Processing helix chain 'J' and resid 35 through 37 No H-bonds generated for 'chain 'J' and resid 35 through 37' Processing helix chain 'J' and resid 61 through 78 removed outlier: 4.228A pdb=" N ARG J 67 " --> pdb=" O THR J 63 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN J 78 " --> pdb=" O GLN J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 129 Processing helix chain 'J' and resid 166 through 178 Processing helix chain 'J' and resid 180 through 189 removed outlier: 3.826A pdb=" N GLU J 189 " --> pdb=" O LYS J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 198 Processing helix chain 'J' and resid 200 through 205 removed outlier: 4.161A pdb=" N ALA J 204 " --> pdb=" O PRO J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 251 through 257 Processing helix chain 'J' and resid 290 through 297 Processing helix chain 'J' and resid 297 through 308 removed outlier: 3.663A pdb=" N ASN J 308 " --> pdb=" O HIS J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 309 through 311 No H-bonds generated for 'chain 'J' and resid 309 through 311' Processing helix chain 'J' and resid 312 through 317 removed outlier: 3.777A pdb=" N VAL J 316 " --> pdb=" O PRO J 312 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 332 Processing helix chain 'J' and resid 335 through 345 removed outlier: 3.564A pdb=" N LYS J 345 " --> pdb=" O TRP J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 353 through 366 Processing helix chain 'J' and resid 374 through 386 removed outlier: 3.909A pdb=" N ILE J 378 " --> pdb=" O THR J 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 386 through 409 Processing helix chain 'J' and resid 414 through 426 removed outlier: 3.520A pdb=" N ILE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 466 through 494 removed outlier: 3.730A pdb=" N SER J 474 " --> pdb=" O HIS J 470 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE J 477 " --> pdb=" O ILE J 473 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER J 478 " --> pdb=" O SER J 474 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG J 479 " --> pdb=" O GLU J 475 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL J 480 " --> pdb=" O ASN J 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 497 through 516 removed outlier: 4.061A pdb=" N SER J 516 " --> pdb=" O GLU J 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 517 through 519 No H-bonds generated for 'chain 'J' and resid 517 through 519' Processing helix chain 'J' and resid 520 through 535 removed outlier: 4.153A pdb=" N PHE J 533 " --> pdb=" O ARG J 529 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU J 534 " --> pdb=" O GLN J 530 " (cutoff:3.500A) Processing helix chain 'J' and resid 540 through 544 removed outlier: 3.543A pdb=" N LEU J 544 " --> pdb=" O ILE J 541 " (cutoff:3.500A) Processing helix chain 'J' and resid 591 through 605 Processing helix chain 'J' and resid 607 through 620 removed outlier: 3.610A pdb=" N SER J 619 " --> pdb=" O MET J 615 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR J 620 " --> pdb=" O PHE J 616 " (cutoff:3.500A) Processing helix chain 'J' and resid 641 through 654 Processing helix chain 'J' and resid 663 through 668 removed outlier: 3.945A pdb=" N THR J 667 " --> pdb=" O ILE J 663 " (cutoff:3.500A) Processing helix chain 'J' and resid 679 through 684 removed outlier: 3.565A pdb=" N LEU J 683 " --> pdb=" O PHE J 680 " (cutoff:3.500A) Processing helix chain 'J' and resid 701 through 709 Processing helix chain 'J' and resid 746 through 752 removed outlier: 3.820A pdb=" N TRP J 750 " --> pdb=" O ASP J 746 " (cutoff:3.500A) Processing helix chain 'J' and resid 777 through 783 removed outlier: 4.340A pdb=" N ILE J 781 " --> pdb=" O ASP J 777 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS J 782 " --> pdb=" O PRO J 778 " (cutoff:3.500A) Processing helix chain 'J' and resid 787 through 810 Processing helix chain 'J' and resid 818 through 833 Processing helix chain 'J' and resid 833 through 842 Processing helix chain 'J' and resid 854 through 870 Processing helix chain 'J' and resid 876 through 886 Processing helix chain 'J' and resid 887 through 891 removed outlier: 4.082A pdb=" N LYS J 891 " --> pdb=" O VAL J 888 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 21 removed outlier: 4.850A pdb=" N ARG K 18 " --> pdb=" O LEU K 14 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 34 Processing helix chain 'K' and resid 35 through 37 No H-bonds generated for 'chain 'K' and resid 35 through 37' Processing helix chain 'K' and resid 61 through 78 removed outlier: 4.006A pdb=" N ARG K 67 " --> pdb=" O THR K 63 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN K 78 " --> pdb=" O GLN K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 130 Processing helix chain 'K' and resid 166 through 178 Processing helix chain 'K' and resid 180 through 189 removed outlier: 3.720A pdb=" N GLU K 189 " --> pdb=" O LYS K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 198 Processing helix chain 'K' and resid 200 through 205 removed outlier: 4.385A pdb=" N ALA K 204 " --> pdb=" O PRO K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 250 Processing helix chain 'K' and resid 251 through 256 Processing helix chain 'K' and resid 288 through 297 Processing helix chain 'K' and resid 297 through 308 removed outlier: 3.971A pdb=" N ASN K 308 " --> pdb=" O HIS K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 310 No H-bonds generated for 'chain 'K' and resid 309 through 310' Processing helix chain 'K' and resid 311 through 316 removed outlier: 3.555A pdb=" N VAL K 316 " --> pdb=" O GLU K 313 " (cutoff:3.500A) Processing helix chain 'K' and resid 317 through 332 Processing helix chain 'K' and resid 335 through 344 Processing helix chain 'K' and resid 346 through 352 removed outlier: 3.786A pdb=" N THR K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 353 through 367 Processing helix chain 'K' and resid 374 through 386 removed outlier: 3.958A pdb=" N ILE K 378 " --> pdb=" O THR K 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 386 through 409 Processing helix chain 'K' and resid 414 through 426 removed outlier: 3.621A pdb=" N ILE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 466 through 494 removed outlier: 3.752A pdb=" N SER K 474 " --> pdb=" O HIS K 470 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE K 477 " --> pdb=" O ILE K 473 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER K 478 " --> pdb=" O SER K 474 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG K 479 " --> pdb=" O GLU K 475 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL K 480 " --> pdb=" O ASN K 476 " (cutoff:3.500A) Processing helix chain 'K' and resid 497 through 516 removed outlier: 4.134A pdb=" N SER K 516 " --> pdb=" O GLU K 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 517 through 519 No H-bonds generated for 'chain 'K' and resid 517 through 519' Processing helix chain 'K' and resid 520 through 535 removed outlier: 4.294A pdb=" N PHE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU K 534 " --> pdb=" O GLN K 530 " (cutoff:3.500A) Processing helix chain 'K' and resid 591 through 605 Processing helix chain 'K' and resid 607 through 620 removed outlier: 3.529A pdb=" N THR K 620 " --> pdb=" O PHE K 616 " (cutoff:3.500A) Processing helix chain 'K' and resid 621 through 623 No H-bonds generated for 'chain 'K' and resid 621 through 623' Processing helix chain 'K' and resid 644 through 654 Processing helix chain 'K' and resid 662 through 667 removed outlier: 3.683A pdb=" N LEU K 666 " --> pdb=" O ILE K 663 " (cutoff:3.500A) Processing helix chain 'K' and resid 680 through 684 Processing helix chain 'K' and resid 701 through 707 Processing helix chain 'K' and resid 746 through 753 removed outlier: 3.810A pdb=" N ARG K 752 " --> pdb=" O GLY K 748 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU K 753 " --> pdb=" O THR K 749 " (cutoff:3.500A) Processing helix chain 'K' and resid 778 through 783 removed outlier: 3.998A pdb=" N HIS K 782 " --> pdb=" O PRO K 778 " (cutoff:3.500A) Processing helix chain 'K' and resid 787 through 810 Processing helix chain 'K' and resid 818 through 833 Processing helix chain 'K' and resid 833 through 842 Processing helix chain 'K' and resid 855 through 870 Processing helix chain 'K' and resid 876 through 886 Processing helix chain 'K' and resid 887 through 891 removed outlier: 3.674A pdb=" N LYS K 891 " --> pdb=" O VAL K 888 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 20 removed outlier: 4.255A pdb=" N ARG M 18 " --> pdb=" O LEU M 14 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 34 Processing helix chain 'M' and resid 35 through 37 No H-bonds generated for 'chain 'M' and resid 35 through 37' Processing helix chain 'M' and resid 61 through 77 removed outlier: 4.165A pdb=" N ARG M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 130 Processing helix chain 'M' and resid 166 through 178 Processing helix chain 'M' and resid 180 through 189 removed outlier: 3.745A pdb=" N GLU M 189 " --> pdb=" O LYS M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 198 Processing helix chain 'M' and resid 200 through 205 removed outlier: 4.369A pdb=" N ALA M 204 " --> pdb=" O PRO M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 250 Processing helix chain 'M' and resid 251 through 256 Processing helix chain 'M' and resid 288 through 297 Processing helix chain 'M' and resid 297 through 308 removed outlier: 3.714A pdb=" N ASN M 308 " --> pdb=" O HIS M 304 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 310 No H-bonds generated for 'chain 'M' and resid 309 through 310' Processing helix chain 'M' and resid 311 through 316 Processing helix chain 'M' and resid 317 through 332 Processing helix chain 'M' and resid 335 through 344 Processing helix chain 'M' and resid 346 through 351 Processing helix chain 'M' and resid 353 through 368 Processing helix chain 'M' and resid 374 through 386 removed outlier: 3.925A pdb=" N ILE M 378 " --> pdb=" O THR M 374 " (cutoff:3.500A) Processing helix chain 'M' and resid 386 through 409 Processing helix chain 'M' and resid 414 through 427 Processing helix chain 'M' and resid 466 through 494 removed outlier: 3.562A pdb=" N SER M 474 " --> pdb=" O HIS M 470 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE M 477 " --> pdb=" O ILE M 473 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER M 478 " --> pdb=" O SER M 474 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG M 479 " --> pdb=" O GLU M 475 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL M 480 " --> pdb=" O ASN M 476 " (cutoff:3.500A) Processing helix chain 'M' and resid 497 through 516 removed outlier: 4.026A pdb=" N SER M 516 " --> pdb=" O GLU M 512 " (cutoff:3.500A) Processing helix chain 'M' and resid 517 through 519 No H-bonds generated for 'chain 'M' and resid 517 through 519' Processing helix chain 'M' and resid 520 through 535 removed outlier: 4.212A pdb=" N PHE M 533 " --> pdb=" O ARG M 529 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU M 534 " --> pdb=" O GLN M 530 " (cutoff:3.500A) Processing helix chain 'M' and resid 591 through 605 Processing helix chain 'M' and resid 607 through 619 Processing helix chain 'M' and resid 620 through 623 Processing helix chain 'M' and resid 641 through 654 Processing helix chain 'M' and resid 680 through 684 removed outlier: 3.635A pdb=" N LEU M 683 " --> pdb=" O PHE M 680 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS M 684 " --> pdb=" O MET M 681 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 680 through 684' Processing helix chain 'M' and resid 701 through 709 Processing helix chain 'M' and resid 748 through 751 Processing helix chain 'M' and resid 783 through 786 Processing helix chain 'M' and resid 787 through 810 Processing helix chain 'M' and resid 818 through 833 Processing helix chain 'M' and resid 833 through 842 Processing helix chain 'M' and resid 855 through 870 Processing helix chain 'M' and resid 876 through 886 removed outlier: 3.604A pdb=" N ASN M 886 " --> pdb=" O GLN M 882 " (cutoff:3.500A) Processing helix chain 'M' and resid 887 through 891 removed outlier: 3.902A pdb=" N LYS M 891 " --> pdb=" O VAL M 888 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 removed outlier: 4.415A pdb=" N THR A 57 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 98 removed outlier: 8.416A pdb=" N SER A 92 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY A 162 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 94 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N HIS A 140 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU A 163 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 11.200A pdb=" N LYS A 138 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 15.735A pdb=" N MET A 165 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 19.552A pdb=" N SER A 136 " --> pdb=" O MET A 165 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 225 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU A 145 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU A 223 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 98 removed outlier: 8.416A pdb=" N SER A 92 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY A 162 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 94 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL A 269 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLY A 162 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.848A pdb=" N TRP A 442 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 550 through 553 Processing sheet with id=AA6, first strand: chain 'A' and resid 658 through 660 removed outlier: 3.531A pdb=" N TYR A 690 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU A 632 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 761 through 762 removed outlier: 6.326A pdb=" N LYS A 761 " --> pdb=" O LYS A 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 906 through 908 removed outlier: 3.575A pdb=" N ARG A 907 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 844 " --> pdb=" O ARG A 907 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AB1, first strand: chain 'B' and resid 39 through 40 removed outlier: 4.436A pdb=" N THR B 57 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 49 " --> pdb=" O TYR B 58 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 92 through 101 removed outlier: 8.551A pdb=" N SER B 92 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLY B 162 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 156 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N HIS B 140 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU B 163 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N LYS B 138 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 15.637A pdb=" N MET B 165 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 19.391A pdb=" N SER B 136 " --> pdb=" O MET B 165 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 225 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU B 145 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU B 223 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 92 through 101 removed outlier: 8.551A pdb=" N SER B 92 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLY B 162 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 156 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N VAL B 269 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY B 162 " --> pdb=" O VAL B 269 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 430 through 434 removed outlier: 3.969A pdb=" N TRP B 442 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 550 through 553 Processing sheet with id=AB6, first strand: chain 'B' and resid 658 through 660 removed outlier: 3.632A pdb=" N TYR B 690 " --> pdb=" O SER B 659 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 735 " --> pdb=" O PHE B 691 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU B 632 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N SER B 736 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TRP B 634 " --> pdb=" O SER B 736 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 761 through 763 Processing sheet with id=AB8, first strand: chain 'B' and resid 844 through 845 Processing sheet with id=AB9, first strand: chain 'B' and resid 853 through 854 removed outlier: 4.270A pdb=" N ILE B 902 " --> pdb=" O GLN B 894 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 894 " --> pdb=" O ILE B 902 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 39 through 40 removed outlier: 4.765A pdb=" N THR C 57 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 49 " --> pdb=" O TYR C 58 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 98 removed outlier: 8.589A pdb=" N SER C 92 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLY C 162 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 94 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N HIS C 140 " --> pdb=" O PRO C 161 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 163 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 11.303A pdb=" N LYS C 138 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 15.530A pdb=" N MET C 165 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 19.474A pdb=" N SER C 136 " --> pdb=" O MET C 165 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU C 145 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU C 223 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 98 removed outlier: 8.589A pdb=" N SER C 92 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLY C 162 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 94 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL C 269 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLY C 162 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 430 through 434 removed outlier: 3.891A pdb=" N TRP C 442 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 550 through 553 Processing sheet with id=AC6, first strand: chain 'C' and resid 658 through 660 removed outlier: 3.531A pdb=" N TYR C 690 " --> pdb=" O SER C 659 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY C 689 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA C 735 " --> pdb=" O GLY C 689 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE C 691 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 632 " --> pdb=" O MET C 732 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 761 through 763 Processing sheet with id=AC8, first strand: chain 'C' and resid 843 through 845 Processing sheet with id=AC9, first strand: chain 'C' and resid 853 through 854 Processing sheet with id=AD1, first strand: chain 'D' and resid 39 through 40 removed outlier: 4.436A pdb=" N THR D 57 " --> pdb=" O THR D 40 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE D 49 " --> pdb=" O TYR D 58 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 92 through 101 removed outlier: 8.588A pdb=" N SER D 92 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLY D 162 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N HIS D 140 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU D 163 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 11.111A pdb=" N LYS D 138 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 15.631A pdb=" N MET D 165 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 19.309A pdb=" N SER D 136 " --> pdb=" O MET D 165 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR D 225 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU D 145 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU D 223 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 92 through 101 removed outlier: 8.588A pdb=" N SER D 92 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLY D 162 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL D 269 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY D 162 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 430 through 434 removed outlier: 3.846A pdb=" N TRP D 442 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 550 through 553 Processing sheet with id=AD6, first strand: chain 'D' and resid 658 through 660 removed outlier: 3.649A pdb=" N TYR D 690 " --> pdb=" O SER D 659 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 735 " --> pdb=" O PHE D 691 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 632 " --> pdb=" O MET D 732 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 699 through 700 Processing sheet with id=AD8, first strand: chain 'D' and resid 761 through 763 Processing sheet with id=AD9, first strand: chain 'D' and resid 906 through 907 Processing sheet with id=AE1, first strand: chain 'D' and resid 893 through 895 Processing sheet with id=AE2, first strand: chain 'E' and resid 39 through 40 removed outlier: 4.379A pdb=" N THR E 57 " --> pdb=" O THR E 40 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS E 56 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE E 49 " --> pdb=" O TYR E 58 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 92 through 101 removed outlier: 8.664A pdb=" N SER E 92 " --> pdb=" O GLY E 162 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY E 162 " --> pdb=" O SER E 92 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N HIS E 140 " --> pdb=" O PRO E 161 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU E 163 " --> pdb=" O LYS E 138 " (cutoff:3.500A) removed outlier: 11.134A pdb=" N LYS E 138 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 15.603A pdb=" N MET E 165 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 19.251A pdb=" N SER E 136 " --> pdb=" O MET E 165 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR E 225 " --> pdb=" O PHE E 143 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU E 145 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU E 223 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 92 through 101 removed outlier: 8.664A pdb=" N SER E 92 " --> pdb=" O GLY E 162 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY E 162 " --> pdb=" O SER E 92 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL E 269 " --> pdb=" O ILE E 160 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY E 162 " --> pdb=" O VAL E 269 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 430 through 434 removed outlier: 3.941A pdb=" N TRP E 442 " --> pdb=" O GLU E 463 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 550 through 553 Processing sheet with id=AE7, first strand: chain 'E' and resid 658 through 661 removed outlier: 3.983A pdb=" N TYR E 690 " --> pdb=" O SER E 659 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU E 632 " --> pdb=" O ALA E 734 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER E 736 " --> pdb=" O LEU E 632 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP E 634 " --> pdb=" O SER E 736 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 699 through 700 Processing sheet with id=AE9, first strand: chain 'E' and resid 761 through 763 Processing sheet with id=AF1, first strand: chain 'E' and resid 906 through 908 Processing sheet with id=AF2, first strand: chain 'E' and resid 853 through 854 removed outlier: 3.574A pdb=" N TYR E 853 " --> pdb=" O LEU E 903 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR E 900 " --> pdb=" O SER E 896 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 39 through 40 removed outlier: 4.321A pdb=" N THR F 57 " --> pdb=" O THR F 40 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE F 49 " --> pdb=" O TYR F 58 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 92 through 98 removed outlier: 8.384A pdb=" N SER F 92 " --> pdb=" O GLY F 162 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLY F 162 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N HIS F 140 " --> pdb=" O PRO F 161 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU F 163 " --> pdb=" O LYS F 138 " (cutoff:3.500A) removed outlier: 11.523A pdb=" N LYS F 138 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 15.786A pdb=" N MET F 165 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 19.132A pdb=" N SER F 136 " --> pdb=" O MET F 165 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR F 225 " --> pdb=" O PHE F 143 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU F 145 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU F 223 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 92 through 98 removed outlier: 8.384A pdb=" N SER F 92 " --> pdb=" O GLY F 162 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLY F 162 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL F 269 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY F 162 " --> pdb=" O VAL F 269 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 430 through 434 removed outlier: 3.790A pdb=" N TRP F 442 " --> pdb=" O GLU F 463 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 550 through 553 Processing sheet with id=AF8, first strand: chain 'F' and resid 658 through 660 removed outlier: 3.985A pdb=" N TYR F 690 " --> pdb=" O SER F 659 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU F 632 " --> pdb=" O ALA F 734 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N SER F 736 " --> pdb=" O LEU F 632 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP F 634 " --> pdb=" O SER F 736 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 699 through 700 Processing sheet with id=AG1, first strand: chain 'F' and resid 761 through 763 Processing sheet with id=AG2, first strand: chain 'F' and resid 906 through 908 Processing sheet with id=AG3, first strand: chain 'F' and resid 853 through 854 removed outlier: 4.465A pdb=" N ILE F 902 " --> pdb=" O GLN F 894 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN F 894 " --> pdb=" O ILE F 902 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 39 through 40 removed outlier: 4.551A pdb=" N THR G 57 " --> pdb=" O THR G 40 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE G 49 " --> pdb=" O TYR G 58 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 91 through 98 removed outlier: 8.676A pdb=" N SER G 92 " --> pdb=" O GLY G 162 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLY G 162 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N HIS G 140 " --> pdb=" O PRO G 161 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU G 163 " --> pdb=" O LYS G 138 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N LYS G 138 " --> pdb=" O LEU G 163 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N HIS G 137 " --> pdb=" O VAL G 230 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL G 230 " --> pdb=" O HIS G 137 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE G 139 " --> pdb=" O GLU G 228 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLU G 228 " --> pdb=" O ILE G 139 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE G 141 " --> pdb=" O GLY G 226 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLY G 226 " --> pdb=" O PHE G 141 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE G 143 " --> pdb=" O LYS G 224 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 91 through 98 removed outlier: 8.676A pdb=" N SER G 92 " --> pdb=" O GLY G 162 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLY G 162 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N VAL G 269 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLY G 162 " --> pdb=" O VAL G 269 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 430 through 434 removed outlier: 3.654A pdb=" N ASP G 433 " --> pdb=" O VAL G 441 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP G 442 " --> pdb=" O GLU G 463 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 550 through 553 Processing sheet with id=AG9, first strand: chain 'G' and resid 658 through 660 removed outlier: 3.865A pdb=" N TYR G 690 " --> pdb=" O SER G 659 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU G 632 " --> pdb=" O ALA G 734 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N SER G 736 " --> pdb=" O LEU G 632 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP G 634 " --> pdb=" O SER G 736 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 699 through 700 Processing sheet with id=AH2, first strand: chain 'G' and resid 906 through 908 Processing sheet with id=AH3, first strand: chain 'G' and resid 893 through 895 removed outlier: 3.661A pdb=" N GLN G 894 " --> pdb=" O ILE G 902 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE G 902 " --> pdb=" O GLN G 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'H' and resid 39 through 40 removed outlier: 4.248A pdb=" N THR H 57 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS H 56 " --> pdb=" O ASN H 51 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE H 49 " --> pdb=" O TYR H 58 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 91 through 98 removed outlier: 8.236A pdb=" N SER H 92 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N GLY H 162 " --> pdb=" O SER H 92 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N HIS H 140 " --> pdb=" O PRO H 161 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU H 163 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N LYS H 138 " --> pdb=" O LEU H 163 " (cutoff:3.500A) removed outlier: 16.041A pdb=" N MET H 165 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 19.502A pdb=" N SER H 136 " --> pdb=" O MET H 165 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR H 225 " --> pdb=" O PHE H 143 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU H 145 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU H 223 " --> pdb=" O LEU H 145 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 91 through 98 removed outlier: 8.236A pdb=" N SER H 92 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N GLY H 162 " --> pdb=" O SER H 92 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL H 269 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY H 162 " --> pdb=" O VAL H 269 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 430 through 434 Processing sheet with id=AH8, first strand: chain 'H' and resid 550 through 553 removed outlier: 3.660A pdb=" N LYS H 566 " --> pdb=" O SER H 559 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 658 through 660 removed outlier: 3.643A pdb=" N SER H 659 " --> pdb=" O TYR H 688 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR H 690 " --> pdb=" O SER H 659 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU H 632 " --> pdb=" O ALA H 734 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER H 736 " --> pdb=" O LEU H 632 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TRP H 634 " --> pdb=" O SER H 736 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 761 through 763 Processing sheet with id=AI2, first strand: chain 'H' and resid 906 through 908 Processing sheet with id=AI3, first strand: chain 'H' and resid 853 through 854 removed outlier: 3.622A pdb=" N TYR H 853 " --> pdb=" O LEU H 903 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE H 902 " --> pdb=" O GLN H 894 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN H 894 " --> pdb=" O ILE H 902 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'I' and resid 39 through 40 removed outlier: 4.333A pdb=" N THR I 57 " --> pdb=" O THR I 40 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'I' and resid 92 through 101 removed outlier: 8.340A pdb=" N SER I 92 " --> pdb=" O GLY I 162 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY I 162 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N HIS I 140 " --> pdb=" O PRO I 161 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU I 163 " --> pdb=" O LYS I 138 " (cutoff:3.500A) removed outlier: 11.517A pdb=" N LYS I 138 " --> pdb=" O LEU I 163 " (cutoff:3.500A) removed outlier: 15.988A pdb=" N MET I 165 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 19.592A pdb=" N SER I 136 " --> pdb=" O MET I 165 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N HIS I 137 " --> pdb=" O VAL I 230 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL I 230 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE I 139 " --> pdb=" O GLU I 228 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU I 228 " --> pdb=" O ILE I 139 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE I 141 " --> pdb=" O GLY I 226 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY I 226 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N PHE I 143 " --> pdb=" O LYS I 224 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'I' and resid 92 through 101 removed outlier: 8.340A pdb=" N SER I 92 " --> pdb=" O GLY I 162 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY I 162 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N VAL I 269 " --> pdb=" O ILE I 160 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY I 162 " --> pdb=" O VAL I 269 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'I' and resid 430 through 434 removed outlier: 4.050A pdb=" N TRP I 442 " --> pdb=" O GLU I 463 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'I' and resid 550 through 553 Processing sheet with id=AI9, first strand: chain 'I' and resid 733 through 736 removed outlier: 5.904A pdb=" N LEU I 632 " --> pdb=" O ALA I 734 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N SER I 736 " --> pdb=" O LEU I 632 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TRP I 634 " --> pdb=" O SER I 736 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'I' and resid 761 through 763 removed outlier: 6.113A pdb=" N LYS I 761 " --> pdb=" O LYS I 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'I' and resid 906 through 908 Processing sheet with id=AJ3, first strand: chain 'I' and resid 853 through 854 removed outlier: 3.981A pdb=" N TYR I 853 " --> pdb=" O LEU I 903 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'J' and resid 39 through 40 removed outlier: 4.546A pdb=" N THR J 57 " --> pdb=" O THR J 40 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE J 49 " --> pdb=" O TYR J 58 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'J' and resid 92 through 101 removed outlier: 8.691A pdb=" N SER J 92 " --> pdb=" O GLY J 162 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N GLY J 162 " --> pdb=" O SER J 92 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU J 159 " --> pdb=" O PHE J 142 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE J 142 " --> pdb=" O LEU J 159 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS J 140 " --> pdb=" O PRO J 161 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU J 163 " --> pdb=" O LYS J 138 " (cutoff:3.500A) removed outlier: 11.353A pdb=" N LYS J 138 " --> pdb=" O LEU J 163 " (cutoff:3.500A) removed outlier: 15.823A pdb=" N MET J 165 " --> pdb=" O SER J 136 " (cutoff:3.500A) removed outlier: 19.574A pdb=" N SER J 136 " --> pdb=" O MET J 165 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N HIS J 137 " --> pdb=" O VAL J 230 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL J 230 " --> pdb=" O HIS J 137 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE J 139 " --> pdb=" O GLU J 228 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU J 228 " --> pdb=" O ILE J 139 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE J 141 " --> pdb=" O GLY J 226 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLY J 226 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N PHE J 143 " --> pdb=" O LYS J 224 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'J' and resid 92 through 101 removed outlier: 8.691A pdb=" N SER J 92 " --> pdb=" O GLY J 162 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N GLY J 162 " --> pdb=" O SER J 92 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N VAL J 269 " --> pdb=" O ILE J 160 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY J 162 " --> pdb=" O VAL J 269 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'J' and resid 430 through 434 removed outlier: 3.672A pdb=" N TRP J 442 " --> pdb=" O GLU J 463 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'J' and resid 550 through 553 Processing sheet with id=AJ9, first strand: chain 'J' and resid 658 through 660 removed outlier: 3.838A pdb=" N TYR J 690 " --> pdb=" O SER J 659 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU J 632 " --> pdb=" O ALA J 734 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N SER J 736 " --> pdb=" O LEU J 632 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP J 634 " --> pdb=" O SER J 736 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'J' and resid 699 through 700 Processing sheet with id=AK2, first strand: chain 'J' and resid 761 through 763 Processing sheet with id=AK3, first strand: chain 'J' and resid 906 through 908 Processing sheet with id=AK4, first strand: chain 'J' and resid 893 through 895 Processing sheet with id=AK5, first strand: chain 'K' and resid 39 through 40 removed outlier: 3.971A pdb=" N THR K 57 " --> pdb=" O THR K 40 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE K 49 " --> pdb=" O TYR K 58 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'K' and resid 92 through 101 removed outlier: 8.417A pdb=" N SER K 92 " --> pdb=" O GLY K 162 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLY K 162 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR K 144 " --> pdb=" O HIS K 157 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N HIS K 140 " --> pdb=" O PRO K 161 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU K 163 " --> pdb=" O LYS K 138 " (cutoff:3.500A) removed outlier: 11.520A pdb=" N LYS K 138 " --> pdb=" O LEU K 163 " (cutoff:3.500A) removed outlier: 15.896A pdb=" N MET K 165 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 19.521A pdb=" N SER K 136 " --> pdb=" O MET K 165 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR K 225 " --> pdb=" O PHE K 143 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU K 145 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU K 223 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'K' and resid 92 through 101 removed outlier: 8.417A pdb=" N SER K 92 " --> pdb=" O GLY K 162 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLY K 162 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL K 269 " --> pdb=" O ILE K 160 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY K 162 " --> pdb=" O VAL K 269 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'K' and resid 430 through 434 removed outlier: 3.824A pdb=" N TRP K 442 " --> pdb=" O GLU K 463 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'K' and resid 550 through 553 Processing sheet with id=AL1, first strand: chain 'K' and resid 735 through 736 removed outlier: 6.721A pdb=" N TRP K 634 " --> pdb=" O SER K 736 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'K' and resid 658 through 660 removed outlier: 3.537A pdb=" N SER K 659 " --> pdb=" O TYR K 688 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR K 690 " --> pdb=" O SER K 659 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'K' and resid 761 through 763 Processing sheet with id=AL4, first strand: chain 'K' and resid 906 through 908 Processing sheet with id=AL5, first strand: chain 'K' and resid 853 through 854 removed outlier: 3.542A pdb=" N TYR K 853 " --> pdb=" O LEU K 903 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'M' and resid 39 through 40 removed outlier: 4.563A pdb=" N THR M 57 " --> pdb=" O THR M 40 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS M 56 " --> pdb=" O ASN M 51 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'M' and resid 92 through 101 removed outlier: 8.301A pdb=" N SER M 92 " --> pdb=" O GLY M 162 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLY M 162 " --> pdb=" O SER M 92 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE M 156 " --> pdb=" O TYR M 98 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N HIS M 140 " --> pdb=" O PRO M 161 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU M 163 " --> pdb=" O LYS M 138 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N LYS M 138 " --> pdb=" O LEU M 163 " (cutoff:3.500A) removed outlier: 15.633A pdb=" N MET M 165 " --> pdb=" O SER M 136 " (cutoff:3.500A) removed outlier: 19.322A pdb=" N SER M 136 " --> pdb=" O MET M 165 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR M 225 " --> pdb=" O PHE M 143 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU M 145 " --> pdb=" O LEU M 223 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU M 223 " --> pdb=" O LEU M 145 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'M' and resid 92 through 101 removed outlier: 8.301A pdb=" N SER M 92 " --> pdb=" O GLY M 162 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLY M 162 " --> pdb=" O SER M 92 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE M 156 " --> pdb=" O TYR M 98 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL M 269 " --> pdb=" O ILE M 160 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY M 162 " --> pdb=" O VAL M 269 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'M' and resid 430 through 434 removed outlier: 3.768A pdb=" N TRP M 442 " --> pdb=" O GLU M 463 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'M' and resid 550 through 553 Processing sheet with id=AM2, first strand: chain 'M' and resid 658 through 660 removed outlier: 6.536A pdb=" N LEU M 632 " --> pdb=" O ALA M 734 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR M 756 " --> pdb=" O LEU M 633 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'M' and resid 761 through 762 removed outlier: 6.356A pdb=" N LYS M 761 " --> pdb=" O LYS M 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM3 Processing sheet with id=AM4, first strand: chain 'M' and resid 906 through 908 Processing sheet with id=AM5, first strand: chain 'M' and resid 853 through 854 4202 hydrogen bonds defined for protein. 11985 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: 42.76 Time building geometry restraints manager: 26.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.54: 80555 1.54 - 1.88: 895 1.88 - 2.22: 0 2.22 - 2.56: 0 2.56 - 2.90: 1 Bond restraints: 81451 Sorted by residual: bond pdb=" C THR H 104 " pdb=" N ALA H 106 " ideal model delta sigma weight residual 1.332 2.897 -1.565 1.40e-02 5.10e+03 1.25e+04 bond pdb=" C GLY C 685 " pdb=" N ARG C 686 " ideal model delta sigma weight residual 1.330 1.239 0.091 1.37e-02 5.33e+03 4.40e+01 bond pdb=" C ILE K 699 " pdb=" N LEU K 700 " ideal model delta sigma weight residual 1.331 1.242 0.089 1.44e-02 4.82e+03 3.81e+01 bond pdb=" N ILE K 663 " pdb=" CA ILE K 663 " ideal model delta sigma weight residual 1.461 1.402 0.060 1.17e-02 7.31e+03 2.59e+01 bond pdb=" C CYS I 119 " pdb=" N HIS I 120 " ideal model delta sigma weight residual 1.335 1.269 0.065 1.36e-02 5.41e+03 2.31e+01 ... (remaining 81446 not shown) Histogram of bond angle deviations from ideal: 79.38 - 93.84: 1 93.84 - 108.30: 3936 108.30 - 122.75: 99362 122.75 - 137.21: 7548 137.21 - 151.66: 1 Bond angle restraints: 110848 Sorted by residual: angle pdb=" O THR H 104 " pdb=" C THR H 104 " pdb=" N ALA H 106 " ideal model delta sigma weight residual 122.03 79.38 42.65 7.30e-01 1.88e+00 3.41e+03 angle pdb=" C THR H 104 " pdb=" N ALA H 106 " pdb=" CA ALA H 106 " ideal model delta sigma weight residual 121.54 151.66 -30.12 1.91e+00 2.74e-01 2.49e+02 angle pdb=" N GLU A 850 " pdb=" CA GLU A 850 " pdb=" C GLU A 850 " ideal model delta sigma weight residual 110.24 98.46 11.78 1.41e+00 5.03e-01 6.98e+01 angle pdb=" N TYR A 853 " pdb=" CA TYR A 853 " pdb=" C TYR A 853 " ideal model delta sigma weight residual 110.53 100.56 9.97 1.32e+00 5.74e-01 5.71e+01 angle pdb=" N LEU B 909 " pdb=" CA LEU B 909 " pdb=" C LEU B 909 " ideal model delta sigma weight residual 109.96 98.77 11.19 1.49e+00 4.50e-01 5.64e+01 ... (remaining 110843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.88: 45710 23.88 - 47.76: 2273 47.76 - 71.63: 187 71.63 - 95.51: 66 95.51 - 119.39: 1 Dihedral angle restraints: 48237 sinusoidal: 17128 harmonic: 31109 Sorted by residual: dihedral pdb=" CA THR H 104 " pdb=" C THR H 104 " pdb=" N ALA H 106 " pdb=" CA ALA H 106 " ideal model delta harmonic sigma weight residual 180.00 60.61 119.39 0 5.00e+00 4.00e-02 5.70e+02 dihedral pdb=" CA PRO H 947 " pdb=" C PRO H 947 " pdb=" N ASN H 948 " pdb=" CA ASN H 948 " ideal model delta harmonic sigma weight residual 180.00 151.08 28.92 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ASN I 128 " pdb=" C ASN I 128 " pdb=" N SER I 129 " pdb=" CA SER I 129 " ideal model delta harmonic sigma weight residual 180.00 151.80 28.20 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 48234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 11022 0.079 - 0.158: 1173 0.158 - 0.236: 80 0.236 - 0.315: 10 0.315 - 0.394: 3 Chirality restraints: 12288 Sorted by residual: chirality pdb=" CA ARG K 18 " pdb=" N ARG K 18 " pdb=" C ARG K 18 " pdb=" CB ARG K 18 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA TYR K 20 " pdb=" N TYR K 20 " pdb=" C TYR K 20 " pdb=" CB TYR K 20 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA LEU A 700 " pdb=" N LEU A 700 " pdb=" C LEU A 700 " pdb=" CB LEU A 700 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 12285 not shown) Planarity restraints: 14292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR H 104 " 0.190 2.00e-02 2.50e+03 2.54e-01 6.44e+02 pdb=" C THR H 104 " -0.429 2.00e-02 2.50e+03 pdb=" O THR H 104 " 0.185 2.00e-02 2.50e+03 pdb=" N ALA H 106 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 942 " -0.083 2.00e-02 2.50e+03 5.47e-02 7.47e+01 pdb=" CG TRP H 942 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP H 942 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP H 942 " 0.068 2.00e-02 2.50e+03 pdb=" NE1 TRP H 942 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP H 942 " 0.028 2.00e-02 2.50e+03 pdb=" CE3 TRP H 942 " 0.065 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 942 " -0.065 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 942 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP H 942 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 943 " -0.102 2.00e-02 2.50e+03 5.37e-02 7.21e+01 pdb=" CG TRP F 943 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP F 943 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP F 943 " 0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP F 943 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 TRP F 943 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP F 943 " 0.066 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 943 " -0.072 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 943 " 0.032 2.00e-02 2.50e+03 pdb=" CH2 TRP F 943 " -0.057 2.00e-02 2.50e+03 ... (remaining 14289 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 8564 2.75 - 3.28: 80840 3.28 - 3.82: 132732 3.82 - 4.36: 148711 4.36 - 4.90: 255788 Nonbonded interactions: 626635 Sorted by model distance: nonbonded pdb=" OG SER K 559 " pdb=" OE1 GLU K 561 " model vdw 2.208 2.440 nonbonded pdb=" O SER K 539 " pdb=" OG1 THR K 543 " model vdw 2.217 2.440 nonbonded pdb=" O ILE A 173 " pdb=" OG SER A 176 " model vdw 2.223 2.440 nonbonded pdb=" O ILE M 126 " pdb=" OG SER M 130 " model vdw 2.233 2.440 nonbonded pdb=" OD1 ASN G 410 " pdb=" OH TYR G 503 " model vdw 2.233 2.440 ... (remaining 626630 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 10 and (name N or name CA or name C or name O or name CB \ )) or resid 11 or (resid 12 through 23 and (name N or name CA or name C or name \ O or name CB )) or resid 24 or (resid 25 through 35 and (name N or name CA or na \ me C or name O or name CB )) or resid 36 through 37 or (resid 38 through 39 and \ (name N or name CA or name C or name O or name CB )) or resid 40 through 45 or ( \ resid 46 through 50 and (name N or name CA or name C or name O or name CB )) or \ resid 51 or (resid 52 through 53 and (name N or name CA or name C or name O or n \ ame CB )) or resid 54 through 56 or (resid 57 through 60 and (name N or name CA \ or name C or name O or name CB )) or resid 61 through 62 or (resid 63 through 64 \ and (name N or name CA or name C or name O or name CB )) or resid 65 or (resid \ 66 through 67 and (name N or name CA or name C or name O or name CB )) or resid \ 68 through 69 or (resid 70 and (name N or name CA or name C or name O or name CB \ )) or resid 71 through 72 or (resid 73 and (name N or name CA or name C or name \ O or name CB )) or resid 74 through 76 or (resid 77 through 78 and (name N or n \ ame CA or name C or name O or name CB )) or resid 79 through 81 or (resid 82 thr \ ough 83 and (name N or name CA or name C or name O or name CB )) or resid 84 or \ (resid 85 and (name N or name CA or name C or name O or name CB )) or resid 86 o \ r (resid 87 and (name N or name CA or name C or name O or name CB )) or resid 88 \ through 91 or (resid 92 and (name N or name CA or name C or name O or name CB ) \ ) or resid 93 or (resid 94 through 97 and (name N or name CA or name C or name O \ or name CB )) or resid 98 through 99 or (resid 100 through 103 and (name N or n \ ame CA or name C or name O or name CB )) or resid 104 or resid 108 through 109 o \ r (resid 110 through 111 and (name N or name CA or name C or name O or name CB ) \ ) or resid 112 through 113 or (resid 114 through 115 and (name N or name CA or n \ ame C or name O or name CB )) or resid 116 through 119 or (resid 120 through 122 \ and (name N or name CA or name C or name O or name CB )) or resid 123 through 1 \ 26 or (resid 127 and (name N or name CA or name C or name O or name CB )) or res \ id 128 or (resid 129 through 130 and (name N or name CA or name C or name O or n \ ame CB )) or resid 131 or (resid 132 and (name N or name CA or name C or name O \ or name CB )) or resid 133 or resid 135 through 137 or (resid 138 through 139 an \ d (name N or name CA or name C or name O or name CB )) or resid 140 through 143 \ or (resid 144 through 146 and (name N or name CA or name C or name O or name CB \ )) or resid 147 or (resid 148 through 151 and (name N or name CA or name C or na \ me O or name CB )) or resid 152 through 157 or (resid 158 through 160 and (name \ N or name CA or name C or name O or name CB )) or resid 161 through 162 or (resi \ d 163 through 167 and (name N or name CA or name C or name O or name CB )) or re \ sid 168 through 169 or (resid 170 through 171 and (name N or name CA or name C o \ r name O or name CB )) or resid 172 through 177 or (resid 178 through 181 and (n \ ame N or name CA or name C or name O or name CB )) or resid 182 through 183 or ( \ resid 184 through 188 and (name N or name CA or name C or name O or name CB )) o \ r resid 189 or (resid 190 and (name N or name CA or name C or name O or name CB \ )) or (resid 191 through 194 and (name N or name CA or name C or name O or name \ CB )) or resid 195 or (resid 196 through 199 and (name N or name CA or name C or \ name O or name CB )) or resid 200 through 205 or (resid 206 through 207 and (na \ me N or name CA or name C or name O or name CB )) or resid 208 through 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 t \ hrough 215 or (resid 216 and (name N or name CA or name C or name O or name CB ) \ ) or resid 217 or (resid 218 through 219 and (name N or name CA or name C or nam \ e O or name CB )) or resid 220 through 223 or (resid 224 and (name N or name CA \ or name C or name O or name CB )) or resid 225 through 229 or (resid 230 and (na \ me N or name CA or name C or name O or name CB )) or (resid 231 and (name N or n \ ame CA or name C or name O )) or (resid 232 and (name N or name CA or name C or \ name O or name CB )) or resid 233 through 236 or (resid 237 through 239 and (nam \ e N or name CA or name C or name O or name CB )) or resid 240 or (resid 241 and \ (name N or name CA or name C or name O or name CB )) or resid 242 or (resid 243 \ through 245 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 6 through 247 or (resid 248 and (name N or name CA or name C or name O or name C \ B )) or resid 249 through 250 or (resid 251 and (name N or name CA or name C or \ name O or name CB )) or resid 252 or (resid 253 and (name N or name CA or name C \ or name O or name CB )) or resid 254 or (resid 255 through 258 and (name N or n \ ame CA or name C or name O or name CB )) or resid 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 26 \ 4 or (resid 265 through 267 and (name N or name CA or name C or name O or name C \ B )) or resid 268 through 269 or (resid 270 and (name N or name CA or name C or \ name O or name CB )) or resid 271 or resid 289 or (resid 290 and (name N or name \ CA or name C or name O or name CB )) or resid 291 or (resid 292 and (name N or \ name CA or name C or name O or name CB )) or resid 293 or (resid 294 through 297 \ and (name N or name CA or name C or name O or name CB )) or resid 298 through 3 \ 00 or (resid 301 through 303 and (name N or name CA or name C or name O or name \ CB )) or resid 304 or (resid 305 through 307 and (name N or name CA or name C or \ name O or name CB )) or resid 308 or (resid 309 through 310 and (name N or name \ CA or name C or name O or name CB )) or resid 311 through 315 or (resid 316 thr \ ough 317 and (name N or name CA or name C or name O or name CB )) or resid 318 t \ hrough 319 or (resid 320 through 321 and (name N or name CA or name C or name O \ or name CB )) or resid 322 through 325 or (resid 326 through 330 and (name N or \ name CA or name C or name O or name CB )) or resid 331 or (resid 332 through 336 \ and (name N or name CA or name C or name O or name CB )) or resid 337 or (resid \ 338 through 340 and (name N or name CA or name C or name O or name CB )) or res \ id 341 through 342 or (resid 343 and (name N or name CA or name C or name O or n \ ame CB )) or resid 344 through 351 or (resid 352 and (name N or name CA or name \ C or name O or name CB )) or resid 353 through 355 or (resid 356 and (name N or \ name CA or name C or name O or name CB )) or resid 357 or (resid 358 and (name N \ or name CA or name C or name O or name CB )) or resid 359 or (resid 360 through \ 361 and (name N or name CA or name C or name O or name CB )) or resid 362 throu \ gh 363 or resid 372 or (resid 373 and (name N or name CA or name C or name O or \ name CB )) or resid 374 or (resid 375 through 376 and (name N or name CA or name \ C or name O or name CB )) or resid 377 or (resid 378 through 379 and (name N or \ name CA or name C or name O or name CB )) or resid 380 through 391 or (resid 39 \ 2 through 393 and (name N or name CA or name C or name O or name CB )) or resid \ 394 through 403 or (resid 404 and (name N or name CA or name C or name O or name \ CB )) or resid 405 or (resid 406 and (name N or name CA or name C or name O or \ name CB )) or resid 407 through 413 or (resid 414 and (name N or name CA or name \ C or name O or name CB )) or resid 415 through 417 or (resid 418 through 419 an \ d (name N or name CA or name C or name O or name CB )) or resid 420 through 421 \ or (resid 422 and (name N or name CA or name C or name O or name CB )) or resid \ 423 through 430 or (resid 431 and (name N or name CA or name C or name O or name \ CB )) or resid 432 or (resid 433 and (name N or name CA or name C or name O or \ name CB )) or resid 434 through 436 or (resid 437 and (name N or name CA or name \ C or name O or name CB )) or resid 438 or (resid 439 and (name N or name CA or \ name C or name O or name CB )) or resid 440 through 451 or (resid 452 through 45 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 455 through \ 456 or (resid 457 and (name N or name CA or name C or name O or name CB )) or re \ sid 458 or (resid 459 and (name N or name CA or name C or name O or name CB )) o \ r resid 460 through 463 or (resid 464 through 465 and (name N or name CA or name \ C or name O or name CB )) or resid 466 through 467 or (resid 468 through 469 an \ d (name N or name CA or name C or name O or name CB )) or resid 470 through 472 \ or (resid 473 and (name N or name CA or name C or name O or name CB )) or resid \ 474 through 477 or (resid 478 through 480 and (name N or name CA or name C or na \ me O or name CB )) or resid 481 through 482 or (resid 483 through 484 and (name \ N or name CA or name C or name O or name CB )) or resid 485 or (resid 486 and (n \ ame N or name CA or name C or name O or name CB )) or resid 487 through 491 or ( \ resid 492 through 493 and (name N or name CA or name C or name O or name CB )) o \ r resid 494 through 496 or (resid 497 and (name N or name CA or name C or name O \ or name CB )) or resid 498 through 499 or (resid 500 and (name N or name CA or \ name C or name O or name CB )) or resid 501 through 504 or (resid 505 and (name \ N or name CA or name C or name O or name CB )) or resid 506 through 508 or (resi \ d 509 through 510 and (name N or name CA or name C or name O or name CB )) or re \ sid 511 or (resid 512 through 513 and (name N or name CA or name C or name O or \ name CB )) or resid 514 or (resid 515 and (name N or name CA or name C or name O \ or name CB )) or resid 516 through 517 or (resid 518 and (name N or name CA or \ name C or name O or name CB )) or resid 519 through 526 or (resid 527 through 52 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 530 through \ 541 or (resid 542 and (name N or name CA or name C or name O or name CB )) or re \ sid 543 or (resid 544 through 545 and (name N or name CA or name C or name O or \ name CB )) or resid 546 through 549 or (resid 550 through 551 and (name N or nam \ e CA or name C or name O or name CB )) or resid 552 through 556 or (resid 557 an \ d (name N or name CA or name C or name O or name CB )) or resid 558 through 559 \ or (resid 560 through 562 and (name N or name CA or name C or name O or name CB \ )) or resid 563 through 564 or (resid 566 through 568 and (name N or name CA or \ name C or name O or name CB )) or resid 569 through 572 or (resid 573 and (name \ N or name CA or name C or name O or name CB )) or resid 574 through 575 or (resi \ d 576 and (name N or name CA or name C or name O or name CB )) or resid 577 or ( \ resid 578 and (name N or name CA or name 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name CA or name C or name O or name CB ) \ ) or resid 485 or (resid 486 and (name N or name CA or name C or name O or name \ CB )) or resid 487 through 491 or (resid 492 through 493 and (name N or name CA \ or name C or name O or name CB )) or resid 494 through 496 or (resid 497 and (na \ me N or name CA or name C or name O or name CB )) or resid 498 through 499 or (r \ esid 500 and (name N or name CA or name C or name O or name CB )) or resid 501 t \ hrough 504 or (resid 505 and (name N or name CA or name C or name O or name CB ) \ ) or resid 506 through 511 or (resid 512 through 513 and (name N or name CA or n \ ame C or name O or name CB )) or resid 514 through 526 or (resid 527 through 529 \ and (name N or name CA or name C or name O or name CB )) or resid 530 through 5 \ 41 or (resid 542 and (name N or name CA or name C or name O or name CB )) or res \ id 543 or (resid 544 through 545 and (name N or name CA or name C or name O or n \ ame CB )) or resid 546 through 549 or (resid 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or name CB )) \ or resid 191 or (resid 192 through 194 and (name N or name CA or name C or name \ O or name CB )) or resid 195 or (resid 196 through 199 and (name N or name CA o \ r name C or name O or name CB )) or resid 200 through 205 or (resid 206 through \ 207 and (name N or name CA or name C or name O or name CB )) or resid 208 throug \ h 209 or (resid 210 and (name N or name CA or name C or name O or name CB )) or \ resid 211 through 214 or (resid 215 through 216 and (name N or name CA or name C \ or name O or name CB )) or resid 217 or (resid 218 through 219 and (name N or n \ ame CA or name C or name O or name CB )) or resid 220 through 223 or (resid 224 \ and (name N or name CA or name C or name O or name CB )) or resid 225 through 23 \ 0 or (resid 231 and (name N or name CA or name C or name O )) or (resid 232 and \ (name N or name CA or name C or name O or name CB )) or resid 233 through 236 or \ (resid 237 through 239 and (name N or name CA or name C or name O or name CB )) \ or resid 240 or (resid 241 and (name N or name CA or name C or name O or name C \ B )) or resid 242 or (resid 243 through 245 and (name N or name CA or name C or \ name O or name CB )) or resid 246 through 247 or (resid 248 and (name N or name \ CA or name C or name O or name CB )) or resid 249 through 250 or (resid 251 and \ (name N or name CA or name C or name O or name CB )) or resid 252 or (resid 253 \ and (name N or name CA or name C or name O or name CB )) or resid 254 or (resid \ 255 through 258 and (name N or name CA or name C or name O or name CB )) or resi \ d 259 or (resid 260 through 262 and (name N or name CA or name C or name O or na \ me CB )) or resid 263 through 264 or (resid 265 through 267 and (name N or name \ CA or name C or name O or name CB )) or resid 268 through 269 or (resid 270 and \ (name N or name CA or name C or name O or name CB )) or resid 271 or resid 289 o \ r (resid 290 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 91 or (resid 292 and (name N or name CA or name C or name O or name CB )) or res \ id 293 or (resid 294 through 297 and (name N or name CA or name C or name O or n \ ame CB )) or resid 298 through 300 or (resid 301 through 303 and (name N or name \ CA or name C or name O or name CB )) or resid 304 or (resid 305 through 307 and \ (name N or name CA or name C or name O or name CB )) or resid 308 through 309 o \ r (resid 310 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 11 through 315 or (resid 316 through 317 and (name N or name CA or name C or nam \ e O or name CB )) or resid 318 through 319 or (resid 320 through 321 and (name N \ or name CA or name C or name O or name CB )) or resid 322 through 325 or (resid \ 326 through 330 and (name N or name CA or name C or name O or name CB )) or res \ id 331 or (resid 332 through 336 and (name N or name CA or name C or name O or n \ ame CB )) or resid 337 or (resid 338 through 340 and (name N or name CA or name \ C or name O or name CB )) or resid 341 through 342 or (resid 343 and (name N or \ name CA or name C or name O or name CB )) or resid 344 through 349 or (resid 350 \ and (name N or name CA or name C or name O or name CB )) or resid 351 or (resid \ 352 and (name N or name CA or name C or name O or name CB )) or resid 353 throu \ gh 355 or (resid 356 and (name N or name CA or name C or name O or name CB )) or \ resid 357 through 360 or (resid 361 and (name N or name CA or name C or name O \ or name CB )) or resid 362 through 363 or resid 372 or (resid 373 and (name N or \ name CA or name C or name O or name CB )) or resid 374 or (resid 375 through 37 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 377 or (resi \ d 378 through 379 and (name N or name CA or name C or name O or name CB )) or re \ sid 380 through 390 or (resid 391 through 393 and (name N or name CA or name C o \ r name O or name CB )) or resid 394 or (resid 395 and (name N or name CA or name \ C or name O or name CB )) or resid 396 through 401 or (resid 402 through 404 an \ d (name N or name CA or name C or name O or name CB )) or resid 405 or (resid 40 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 407 through \ 413 or (resid 414 and (name N or name CA or name C or name O or name CB )) or re \ sid 415 through 417 or (resid 418 through 419 and (name N or name CA or name C o \ r name O or name CB )) or resid 420 or (resid 421 through 422 and (name N or nam \ e CA or name C or name O or name CB )) or resid 423 through 424 or (resid 425 th \ rough 426 and (name N or name CA or name C or name O or name CB )) or resid 427 \ through 430 or (resid 431 and (name N or name CA or name C or name O or name CB \ )) or resid 432 or (resid 433 and (name N or name CA or name C or name O or name \ CB )) or resid 434 through 436 or (resid 437 and (name N or name CA or name C o \ r name O or name CB )) or resid 438 or (resid 439 and (name N or name CA or name \ C or name O or name CB )) or resid 440 through 451 or (resid 452 through 454 an \ d (name N or name CA or name C or name O or name CB )) or resid 455 through 458 \ or (resid 459 and (name N or name CA or name C or name O or name CB )) or resid \ 460 through 463 or (resid 464 through 465 and (name N or name CA or name C or na \ me O or name CB )) or resid 466 through 467 or (resid 468 through 469 and (name \ N or name CA or name C or name O or name CB )) or resid 470 through 472 or (resi \ d 473 and (name N or name CA or name C or name O or name CB )) or resid 474 thro \ ugh 477 or (resid 478 through 480 and (name N or name CA or name C or name O or \ name CB )) or resid 481 through 482 or (resid 483 through 484 and (name N or nam \ e CA or name C or name O or name CB )) or resid 485 or (resid 486 and (name N or \ name CA or name C or name O or name CB )) or resid 487 through 491 or (resid 49 \ 2 through 493 and (name N or name CA or name C or name O or name CB )) or resid \ 494 through 496 or (resid 497 and (name N or name CA or name C or name O or name \ CB )) or resid 498 through 499 or (resid 500 and (name N or name CA or name C o \ r name O or name CB )) or resid 501 through 504 or (resid 505 and (name N or nam \ e CA or name C or name O or name CB )) or resid 506 through 508 or (resid 509 th \ rough 510 and (name N or name CA or name C or name O or name CB )) or resid 511 \ or (resid 512 through 513 and (name N or name CA or name C or name O or name CB \ )) or resid 514 or (resid 515 and (name N or name CA or name C or name O or name \ CB )) or resid 516 through 517 or (resid 518 and (name N or name CA or name C o \ r name O or name CB )) or resid 519 through 526 or (resid 527 through 529 and (n \ ame N or name CA or name C or name O or name CB )) or resid 530 through 541 or ( \ resid 542 and (name N or name CA or name C or name O or name CB )) or resid 543 \ or (resid 544 through 545 and (name N or name CA or name C or name O or name CB \ )) or resid 546 through 550 or (resid 551 and (name N or name CA or name C or na \ me O or name CB )) or resid 552 through 556 or (resid 557 and (name N or name CA \ or name C or name O or name CB )) or resid 558 through 560 or (resid 561 throug \ h 562 and (name N or name CA or name C or name O or name CB )) or resid 563 thro \ ugh 564 or (resid 566 through 568 and (name N or name CA or name C or name O or \ name CB )) or resid 569 through 572 or (resid 573 and (name N or name CA or name \ C or name O or name CB )) or resid 574 through 575 or (resid 576 and (name N or \ name CA or name C or name O or name CB )) or resid 577 or (resid 578 and (name \ N or name CA or name C or name O or name CB )) or resid 579 through 581 or (resi \ d 582 and (name N or name CA or name C or name O or name CB )) or resid 583 thro \ ugh 584 or (resid 585 through 620 and (name N or name CA or name C or name O or \ name CB )) or (resid 622 through 624 and (name N or name CA or name C or name O \ or name CB )) or resid 625 or (resid 626 through 627 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 633 through 635 and (name N or name CA o \ r name C or name O or name CB )) or resid 636 through 638 or (resid 639 through \ 640 and (name N or name CA or name C or name O or name CB )) or (resid 643 throu \ gh 653 and (name N or name CA or name C or name O or name CB )) or resid 654 or \ (resid 655 through 656 and (name N or name CA or name C or name O or name CB )) \ or (resid 668 and (name N or name CA or name C or name O or name CB )) or (resid \ 680 through 684 and (name N or name CA or name C or name O or name CB )) or res \ id 685 or (resid 686 and (name N or name CA or name C or name O or name CB )) or \ resid 687 or (resid 688 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 689 through 691 and (name N or name CA or name C or name O or name C \ B )) or resid 699 through 708 or (resid 729 through 747 and (name N or name CA o \ r name C or name O or name CB )) or resid 748 or (resid 749 through 763 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 779 through 810 and ( \ name N or name CA or name C or name O or name CB )) or resid 811 or (resid 812 t \ hrough 847 and (name N or name CA or name C or name O or name CB )) or resid 852 \ or (resid 853 and (name N or name CA or name C or name O )) or resid 854 throug \ h 876 or resid 878 through 916 or resid 919 through 922 or resid 937 through 949 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 5.370 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: 0.070 Extract box with map and model: 23.350 Check model and map are aligned: 0.870 Set scattering table: 0.550 Process input model: 174.620 Find NCS groups from input model: 5.920 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 213.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.007 1.565 81451 Z= 0.511 Angle : 0.770 42.646 110848 Z= 0.516 Chirality : 0.048 0.394 12288 Planarity : 0.005 0.254 14292 Dihedral : 13.655 119.390 28073 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.45 % Allowed : 1.21 % Favored : 98.34 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.08), residues: 10345 helix: 1.66 (0.08), residues: 4743 sheet: -0.27 (0.14), residues: 1412 loop : 0.25 (0.10), residues: 4190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.003 TRP F 943 HIS 0.012 0.001 HIS I 125 PHE 0.053 0.002 PHE H 616 TYR 0.109 0.003 TYR K 20 ARG 0.008 0.001 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 742 time to evaluate : 6.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 CYS cc_start: 0.7980 (m) cc_final: 0.7735 (m) REVERT: A 437 ASN cc_start: 0.8310 (m110) cc_final: 0.7993 (t0) REVERT: A 732 MET cc_start: 0.7931 (tpt) cc_final: 0.7511 (tmm) REVERT: B 865 TRP cc_start: 0.6002 (t60) cc_final: 0.5693 (t60) REVERT: C 404 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6830 (tm-30) REVERT: D 680 PHE cc_start: 0.5915 (p90) cc_final: 0.5231 (p90) REVERT: D 681 MET cc_start: 0.8150 (mmm) cc_final: 0.7721 (mmm) REVERT: D 879 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7722 (mm-30) REVERT: E 350 TRP cc_start: 0.6955 (t-100) cc_final: 0.6715 (t-100) REVERT: F 680 PHE cc_start: 0.6470 (t80) cc_final: 0.6184 (t80) REVERT: G 541 ILE cc_start: 0.8770 (mm) cc_final: 0.8465 (mm) REVERT: G 615 MET cc_start: 0.8383 (mmp) cc_final: 0.8072 (mmp) REVERT: G 740 PHE cc_start: 0.7431 (m-80) cc_final: 0.7061 (m-80) REVERT: H 294 MET cc_start: 0.6728 (tmm) cc_final: 0.6330 (tmm) REVERT: H 467 ASP cc_start: 0.7215 (m-30) cc_final: 0.6957 (m-30) REVERT: H 759 LYS cc_start: 0.5628 (mptt) cc_final: 0.3504 (ttpt) REVERT: I 165 MET cc_start: 0.8259 (pmm) cc_final: 0.7765 (pmm) REVERT: I 426 MET cc_start: 0.8385 (mmm) cc_final: 0.8132 (mtp) REVERT: J 299 GLU cc_start: 0.8264 (tp30) cc_final: 0.7990 (pm20) REVERT: K 439 LYS cc_start: 0.8508 (ttpp) cc_final: 0.8305 (tttp) REVERT: K 795 PHE cc_start: 0.7370 (t80) cc_final: 0.6821 (t80) REVERT: M 14 LEU cc_start: 0.9169 (tp) cc_final: 0.8897 (tp) REVERT: M 631 MET cc_start: 0.7050 (mpp) cc_final: 0.6351 (tmm) REVERT: M 686 ARG cc_start: 0.8461 (mmp80) cc_final: 0.8119 (mpp-170) REVERT: M 798 LEU cc_start: 0.8981 (mt) cc_final: 0.8775 (mt) outliers start: 34 outliers final: 6 residues processed: 768 average time/residue: 0.7145 time to fit residues: 950.1980 Evaluate side-chains 559 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 553 time to evaluate : 6.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain D residue 634 TRP Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain M residue 524 LYS Chi-restraints excluded: chain M residue 635 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 887 optimal weight: 0.0030 chunk 796 optimal weight: 3.9990 chunk 442 optimal weight: 0.0980 chunk 272 optimal weight: 3.9990 chunk 537 optimal weight: 0.9990 chunk 425 optimal weight: 5.9990 chunk 823 optimal weight: 2.9990 chunk 318 optimal weight: 2.9990 chunk 500 optimal weight: 1.9990 chunk 613 optimal weight: 20.0000 chunk 954 optimal weight: 5.9990 overall best weight: 1.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 363 ASN B 437 ASN C 363 ASN C 755 HIS C 882 GLN D 755 HIS F 188 HIS F 363 ASN ** G 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 453 ASN H 491 HIS H 577 HIS ** I 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 577 HIS J 437 ASN J 491 HIS J 494 GLN ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 HIS M 151 GLN M 296 HIS M 450 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 81451 Z= 0.188 Angle : 0.503 8.409 110848 Z= 0.267 Chirality : 0.041 0.173 12288 Planarity : 0.003 0.068 14292 Dihedral : 3.940 57.537 11263 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.86 % Allowed : 5.86 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.08), residues: 10347 helix: 2.03 (0.08), residues: 4803 sheet: -0.30 (0.14), residues: 1463 loop : 0.41 (0.10), residues: 4081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 865 HIS 0.012 0.001 HIS K 188 PHE 0.035 0.001 PHE D 817 TYR 0.033 0.001 TYR I 20 ARG 0.005 0.000 ARG B 907 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 600 time to evaluate : 7.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 CYS cc_start: 0.7926 (m) cc_final: 0.7721 (m) REVERT: A 437 ASN cc_start: 0.8246 (m110) cc_final: 0.7991 (t0) REVERT: A 615 MET cc_start: 0.8374 (ttm) cc_final: 0.8162 (ttm) REVERT: A 801 PHE cc_start: 0.8224 (m-80) cc_final: 0.7491 (m-10) REVERT: D 350 TRP cc_start: 0.8071 (t-100) cc_final: 0.7678 (t-100) REVERT: D 680 PHE cc_start: 0.6080 (p90) cc_final: 0.5395 (p90) REVERT: D 681 MET cc_start: 0.8441 (mmm) cc_final: 0.8136 (mmm) REVERT: E 84 PHE cc_start: 0.7989 (m-80) cc_final: 0.7741 (m-80) REVERT: G 95 MET cc_start: 0.8539 (tmm) cc_final: 0.7910 (tmm) REVERT: G 541 ILE cc_start: 0.8637 (mm) cc_final: 0.8411 (mm) REVERT: G 740 PHE cc_start: 0.7577 (m-80) cc_final: 0.7245 (m-80) REVERT: G 864 GLU cc_start: 0.8309 (mp0) cc_final: 0.7985 (pp20) REVERT: H 294 MET cc_start: 0.6609 (tmm) cc_final: 0.6233 (tmm) REVERT: H 759 LYS cc_start: 0.5521 (mptt) cc_final: 0.3273 (ttpt) REVERT: J 95 MET cc_start: 0.8086 (tmm) cc_final: 0.7871 (tmm) REVERT: J 232 ASP cc_start: 0.6966 (t0) cc_final: 0.6728 (p0) REVERT: J 299 GLU cc_start: 0.8196 (tp30) cc_final: 0.7960 (pm20) REVERT: K 439 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8339 (tttp) REVERT: K 795 PHE cc_start: 0.7294 (t80) cc_final: 0.6731 (t80) REVERT: M 631 MET cc_start: 0.7461 (mpp) cc_final: 0.6611 (tmm) outliers start: 65 outliers final: 35 residues processed: 639 average time/residue: 0.6988 time to fit residues: 789.4626 Evaluate side-chains 567 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 532 time to evaluate : 6.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 763 CYS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 790 CYS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 879 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain F residue 439 LYS Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 732 MET Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 469 LEU Chi-restraints excluded: chain J residue 581 HIS Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 615 MET Chi-restraints excluded: chain M residue 151 GLN Chi-restraints excluded: chain M residue 296 HIS Chi-restraints excluded: chain M residue 635 LEU Chi-restraints excluded: chain M residue 639 CYS Chi-restraints excluded: chain M residue 667 THR Chi-restraints excluded: chain M residue 790 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 530 optimal weight: 0.9980 chunk 296 optimal weight: 7.9990 chunk 794 optimal weight: 4.9990 chunk 649 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 chunk 956 optimal weight: 20.0000 chunk 1032 optimal weight: 20.0000 chunk 851 optimal weight: 9.9990 chunk 948 optimal weight: 0.0670 chunk 325 optimal weight: 1.9990 chunk 767 optimal weight: 20.0000 overall best weight: 3.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 ASN B 437 ASN B 886 ASN C 288 HIS C 363 ASN C 487 HIS D 304 HIS D 363 ASN D 487 HIS E 363 ASN F 363 ASN G 363 ASN H 344 GLN I 120 HIS I 217 ASN I 491 HIS I 577 HIS J 410 ASN J 450 GLN K 137 HIS ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 363 ASN M 363 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 81451 Z= 0.379 Angle : 0.587 13.104 110848 Z= 0.311 Chirality : 0.043 0.155 12288 Planarity : 0.004 0.060 14292 Dihedral : 4.093 58.354 11250 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.29 % Allowed : 9.29 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.08), residues: 10347 helix: 1.85 (0.07), residues: 4789 sheet: -0.61 (0.13), residues: 1516 loop : 0.27 (0.10), residues: 4042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 634 HIS 0.015 0.002 HIS M 296 PHE 0.034 0.002 PHE C 794 TYR 0.025 0.002 TYR D 20 ARG 0.015 0.001 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 535 time to evaluate : 6.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 CYS cc_start: 0.8048 (m) cc_final: 0.7815 (m) REVERT: A 437 ASN cc_start: 0.8267 (m110) cc_final: 0.7982 (t0) REVERT: D 294 MET cc_start: 0.8079 (mmt) cc_final: 0.7802 (mmt) REVERT: D 680 PHE cc_start: 0.6180 (p90) cc_final: 0.5448 (p90) REVERT: D 681 MET cc_start: 0.8592 (mmm) cc_final: 0.8285 (mmm) REVERT: D 732 MET cc_start: 0.7498 (mmm) cc_final: 0.7169 (mtp) REVERT: G 95 MET cc_start: 0.8481 (tmm) cc_final: 0.7753 (tmm) REVERT: H 294 MET cc_start: 0.6863 (tmm) cc_final: 0.6655 (tmm) REVERT: H 759 LYS cc_start: 0.5160 (mptt) cc_final: 0.2139 (ttpt) REVERT: J 299 GLU cc_start: 0.8303 (tp30) cc_final: 0.8011 (pm20) REVERT: K 439 LYS cc_start: 0.8610 (ttpp) cc_final: 0.8375 (tttp) REVERT: M 475 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6766 (mp0) outliers start: 98 outliers final: 59 residues processed: 603 average time/residue: 0.6875 time to fit residues: 735.8660 Evaluate side-chains 563 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 503 time to evaluate : 6.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 763 CYS Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 790 CYS Chi-restraints excluded: chain B residue 865 TRP Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 738 TYR Chi-restraints excluded: chain D residue 871 ASN Chi-restraints excluded: chain D residue 898 ASN Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 612 LEU Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 439 LYS Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 732 MET Chi-restraints excluded: chain F residue 782 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 202 HIS Chi-restraints excluded: chain G residue 464 VAL Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 801 PHE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 485 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 246 ASN Chi-restraints excluded: chain I residue 583 CYS Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 469 LEU Chi-restraints excluded: chain J residue 581 HIS Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 615 MET Chi-restraints excluded: chain M residue 151 GLN Chi-restraints excluded: chain M residue 417 MET Chi-restraints excluded: chain M residue 475 GLU Chi-restraints excluded: chain M residue 635 LEU Chi-restraints excluded: chain M residue 639 CYS Chi-restraints excluded: chain M residue 790 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 944 optimal weight: 7.9990 chunk 718 optimal weight: 2.9990 chunk 496 optimal weight: 0.0970 chunk 105 optimal weight: 5.9990 chunk 456 optimal weight: 0.0000 chunk 642 optimal weight: 0.0040 chunk 959 optimal weight: 5.9990 chunk 1015 optimal weight: 0.9980 chunk 501 optimal weight: 7.9990 chunk 909 optimal weight: 7.9990 chunk 273 optimal weight: 3.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN C 194 ASN C 288 HIS C 487 HIS D 217 ASN F 363 ASN I 577 HIS J 450 GLN ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 363 ASN K 491 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 81451 Z= 0.148 Angle : 0.467 10.102 110848 Z= 0.245 Chirality : 0.040 0.182 12288 Planarity : 0.003 0.057 14292 Dihedral : 3.701 59.009 11250 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.83 % Allowed : 11.13 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.08), residues: 10347 helix: 2.21 (0.08), residues: 4809 sheet: -0.46 (0.13), residues: 1494 loop : 0.40 (0.10), residues: 4044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 341 HIS 0.006 0.001 HIS I 577 PHE 0.022 0.001 PHE A 801 TYR 0.027 0.001 TYR F 20 ARG 0.014 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 559 time to evaluate : 6.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 CYS cc_start: 0.7932 (m) cc_final: 0.7720 (m) REVERT: A 437 ASN cc_start: 0.8229 (m110) cc_final: 0.7982 (t0) REVERT: A 634 TRP cc_start: 0.8525 (t60) cc_final: 0.8272 (t60) REVERT: C 395 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: D 294 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7553 (mmt) REVERT: D 708 MET cc_start: 0.8681 (tpp) cc_final: 0.8427 (tpp) REVERT: E 937 GLU cc_start: 0.4800 (OUTLIER) cc_final: 0.3381 (tp30) REVERT: G 95 MET cc_start: 0.8522 (tmm) cc_final: 0.7834 (tmm) REVERT: G 631 MET cc_start: 0.6647 (tpp) cc_final: 0.6414 (tpt) REVERT: H 759 LYS cc_start: 0.5117 (mptt) cc_final: 0.2552 (ttpt) REVERT: H 797 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7833 (mm) REVERT: I 590 GLU cc_start: 0.7656 (pp20) cc_final: 0.7313 (pt0) REVERT: J 299 GLU cc_start: 0.8242 (tp30) cc_final: 0.7988 (pm20) REVERT: J 425 MET cc_start: 0.8229 (ttm) cc_final: 0.7976 (ttp) REVERT: K 340 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: K 439 LYS cc_start: 0.8571 (ttpp) cc_final: 0.8359 (tttp) REVERT: M 95 MET cc_start: 0.7952 (tmm) cc_final: 0.7678 (tmm) REVERT: M 598 LEU cc_start: 0.6922 (mt) cc_final: 0.6530 (tp) REVERT: M 631 MET cc_start: 0.7025 (mpp) cc_final: 0.6480 (tmm) REVERT: M 635 LEU cc_start: 0.4789 (OUTLIER) cc_final: 0.3982 (mm) outliers start: 63 outliers final: 40 residues processed: 600 average time/residue: 0.6746 time to fit residues: 722.6873 Evaluate side-chains 561 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 515 time to evaluate : 6.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 763 CYS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 865 TRP Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 879 GLU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 738 TYR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 937 GLU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 439 LYS Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 732 MET Chi-restraints excluded: chain F residue 782 HIS Chi-restraints excluded: chain G residue 202 HIS Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 645 LEU Chi-restraints excluded: chain H residue 485 THR Chi-restraints excluded: chain H residue 797 ILE Chi-restraints excluded: chain I residue 583 CYS Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 581 HIS Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain M residue 417 MET Chi-restraints excluded: chain M residue 512 GLU Chi-restraints excluded: chain M residue 635 LEU Chi-restraints excluded: chain M residue 639 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 846 optimal weight: 4.9990 chunk 576 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 756 optimal weight: 3.9990 chunk 419 optimal weight: 8.9990 chunk 866 optimal weight: 20.0000 chunk 702 optimal weight: 0.4980 chunk 1 optimal weight: 6.9990 chunk 518 optimal weight: 7.9990 chunk 911 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN B 140 HIS B 542 GLN C 288 HIS C 487 HIS ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 HIS E 747 HIS F 246 ASN G 218 HIS G 363 ASN ** G 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 HIS I 577 HIS J 137 HIS J 465 ASN ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 363 ASN M 151 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 81451 Z= 0.382 Angle : 0.575 13.958 110848 Z= 0.304 Chirality : 0.042 0.204 12288 Planarity : 0.004 0.059 14292 Dihedral : 4.037 57.943 11250 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.73 % Allowed : 11.85 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.08), residues: 10347 helix: 1.92 (0.08), residues: 4807 sheet: -0.68 (0.13), residues: 1476 loop : 0.19 (0.10), residues: 4064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 350 HIS 0.010 0.001 HIS I 487 PHE 0.031 0.002 PHE A 801 TYR 0.023 0.002 TYR K 20 ARG 0.006 0.001 ARG H 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 524 time to evaluate : 6.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 CYS cc_start: 0.8065 (m) cc_final: 0.7826 (m) REVERT: A 634 TRP cc_start: 0.8563 (t60) cc_final: 0.8218 (t60) REVERT: C 294 MET cc_start: 0.8031 (tpp) cc_final: 0.7789 (ttt) REVERT: C 395 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: C 704 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8628 (mmt90) REVERT: D 294 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7557 (mmt) REVERT: E 728 MET cc_start: 0.6992 (tpp) cc_final: 0.5472 (ppp) REVERT: E 937 GLU cc_start: 0.5053 (OUTLIER) cc_final: 0.4446 (tp30) REVERT: G 81 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8728 (pp) REVERT: G 486 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: J 299 GLU cc_start: 0.8296 (tp30) cc_final: 0.8021 (pm20) REVERT: K 340 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: K 439 LYS cc_start: 0.8601 (ttpp) cc_final: 0.8364 (tttp) REVERT: K 815 LYS cc_start: 0.7716 (mttp) cc_final: 0.7270 (mmtm) REVERT: M 95 MET cc_start: 0.8051 (tmm) cc_final: 0.7785 (tmm) REVERT: M 635 LEU cc_start: 0.4901 (OUTLIER) cc_final: 0.4037 (mm) outliers start: 131 outliers final: 85 residues processed: 622 average time/residue: 0.6822 time to fit residues: 756.6134 Evaluate side-chains 594 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 501 time to evaluate : 6.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 763 CYS Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 790 CYS Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 704 ARG Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 490 TYR Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 738 TYR Chi-restraints excluded: chain D residue 871 ASN Chi-restraints excluded: chain D residue 898 ASN Chi-restraints excluded: chain D residue 921 TYR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 612 LEU Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 937 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 439 LYS Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 732 MET Chi-restraints excluded: chain F residue 782 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 202 HIS Chi-restraints excluded: chain G residue 464 VAL Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 541 ILE Chi-restraints excluded: chain G residue 645 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 485 THR Chi-restraints excluded: chain H residue 491 HIS Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 246 ASN Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 462 LYS Chi-restraints excluded: chain I residue 501 LEU Chi-restraints excluded: chain I residue 583 CYS Chi-restraints excluded: chain I residue 729 THR Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 469 LEU Chi-restraints excluded: chain J residue 551 LEU Chi-restraints excluded: chain J residue 581 HIS Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 241 ILE Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 551 LEU Chi-restraints excluded: chain K residue 614 ILE Chi-restraints excluded: chain M residue 20 TYR Chi-restraints excluded: chain M residue 217 ASN Chi-restraints excluded: chain M residue 417 MET Chi-restraints excluded: chain M residue 434 VAL Chi-restraints excluded: chain M residue 512 GLU Chi-restraints excluded: chain M residue 551 LEU Chi-restraints excluded: chain M residue 635 LEU Chi-restraints excluded: chain M residue 639 CYS Chi-restraints excluded: chain M residue 790 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 341 optimal weight: 4.9990 chunk 914 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 596 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 1016 optimal weight: 5.9990 chunk 844 optimal weight: 10.0000 chunk 470 optimal weight: 0.4980 chunk 84 optimal weight: 10.0000 chunk 336 optimal weight: 4.9990 chunk 533 optimal weight: 8.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 HIS F 13 GLN H 737 ASN I 140 HIS I 577 HIS ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 491 HIS M 151 GLN M 450 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 81451 Z= 0.376 Angle : 0.575 13.918 110848 Z= 0.303 Chirality : 0.043 0.196 12288 Planarity : 0.004 0.060 14292 Dihedral : 4.161 57.611 11250 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.02 % Allowed : 13.37 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.08), residues: 10347 helix: 1.78 (0.07), residues: 4802 sheet: -0.82 (0.13), residues: 1434 loop : -0.00 (0.10), residues: 4111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 350 HIS 0.018 0.001 HIS D 218 PHE 0.034 0.002 PHE A 801 TYR 0.029 0.002 TYR H 472 ARG 0.006 0.001 ARG H 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 508 time to evaluate : 7.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 CYS cc_start: 0.8042 (m) cc_final: 0.7809 (m) REVERT: A 634 TRP cc_start: 0.8456 (t60) cc_final: 0.8047 (t60) REVERT: C 395 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: C 704 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8673 (mmt90) REVERT: D 294 MET cc_start: 0.8066 (mmt) cc_final: 0.7621 (mmt) REVERT: D 772 TYR cc_start: 0.6905 (m-10) cc_final: 0.6564 (m-10) REVERT: E 667 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7562 (p) REVERT: E 728 MET cc_start: 0.6678 (tpp) cc_final: 0.5582 (ppp) REVERT: E 739 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7881 (t0) REVERT: E 937 GLU cc_start: 0.5138 (OUTLIER) cc_final: 0.4688 (tp30) REVERT: F 704 ARG cc_start: 0.7687 (mmt-90) cc_final: 0.7374 (tpp80) REVERT: F 732 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7632 (tpt) REVERT: G 81 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8703 (pp) REVERT: G 95 MET cc_start: 0.8507 (tmm) cc_final: 0.8025 (tmm) REVERT: G 486 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: J 294 MET cc_start: 0.6527 (tpt) cc_final: 0.6316 (tpp) REVERT: J 299 GLU cc_start: 0.8277 (tp30) cc_final: 0.7997 (pm20) REVERT: J 481 MET cc_start: 0.8750 (mmm) cc_final: 0.8441 (mmt) REVERT: K 340 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: K 439 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8388 (tttp) REVERT: K 795 PHE cc_start: 0.6953 (t80) cc_final: 0.6340 (t80) REVERT: M 95 MET cc_start: 0.8032 (tmm) cc_final: 0.7700 (tmm) REVERT: M 631 MET cc_start: 0.6514 (mpp) cc_final: 0.6154 (mtt) REVERT: M 635 LEU cc_start: 0.4931 (OUTLIER) cc_final: 0.4249 (mm) outliers start: 153 outliers final: 109 residues processed: 623 average time/residue: 0.6698 time to fit residues: 750.6201 Evaluate side-chains 611 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 492 time to evaluate : 6.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 763 CYS Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 790 CYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 704 ARG Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 490 TYR Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 738 TYR Chi-restraints excluded: chain D residue 871 ASN Chi-restraints excluded: chain D residue 898 ASN Chi-restraints excluded: chain D residue 921 TYR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 437 ASN Chi-restraints excluded: chain E residue 612 LEU Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain E residue 729 THR Chi-restraints excluded: chain E residue 739 ASN Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain E residue 937 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 439 LYS Chi-restraints excluded: chain F residue 699 ILE Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 732 MET Chi-restraints excluded: chain F residue 782 HIS Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 202 HIS Chi-restraints excluded: chain G residue 464 VAL Chi-restraints excluded: chain G residue 467 ASP Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 541 ILE Chi-restraints excluded: chain G residue 569 ASN Chi-restraints excluded: chain G residue 645 LEU Chi-restraints excluded: chain G residue 728 MET Chi-restraints excluded: chain G residue 843 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain H residue 485 THR Chi-restraints excluded: chain H residue 491 HIS Chi-restraints excluded: chain H residue 612 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 246 ASN Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 462 LYS Chi-restraints excluded: chain I residue 501 LEU Chi-restraints excluded: chain I residue 583 CYS Chi-restraints excluded: chain I residue 729 THR Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 437 ASN Chi-restraints excluded: chain J residue 469 LEU Chi-restraints excluded: chain J residue 482 ASP Chi-restraints excluded: chain J residue 545 ASP Chi-restraints excluded: chain J residue 581 HIS Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 241 ILE Chi-restraints excluded: chain K residue 247 ILE Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 551 LEU Chi-restraints excluded: chain K residue 568 ILE Chi-restraints excluded: chain K residue 614 ILE Chi-restraints excluded: chain M residue 20 TYR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 217 ASN Chi-restraints excluded: chain M residue 406 VAL Chi-restraints excluded: chain M residue 417 MET Chi-restraints excluded: chain M residue 512 GLU Chi-restraints excluded: chain M residue 551 LEU Chi-restraints excluded: chain M residue 635 LEU Chi-restraints excluded: chain M residue 639 CYS Chi-restraints excluded: chain M residue 790 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 980 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 579 optimal weight: 2.9990 chunk 742 optimal weight: 0.6980 chunk 575 optimal weight: 0.6980 chunk 856 optimal weight: 3.9990 chunk 567 optimal weight: 0.8980 chunk 1012 optimal weight: 0.6980 chunk 633 optimal weight: 1.9990 chunk 617 optimal weight: 3.9990 chunk 467 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN C 288 HIS C 363 ASN D 836 HIS F 246 ASN G 25 GLN ** H 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 577 HIS ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 491 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 81451 Z= 0.170 Angle : 0.493 14.277 110848 Z= 0.254 Chirality : 0.040 0.259 12288 Planarity : 0.003 0.058 14292 Dihedral : 3.814 59.781 11250 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.30 % Allowed : 14.44 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.08), residues: 10347 helix: 2.14 (0.08), residues: 4812 sheet: -0.73 (0.13), residues: 1459 loop : 0.16 (0.10), residues: 4076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 350 HIS 0.008 0.001 HIS I 487 PHE 0.035 0.001 PHE F 801 TYR 0.023 0.001 TYR C 20 ARG 0.006 0.000 ARG H 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 532 time to evaluate : 6.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 634 TRP cc_start: 0.8489 (t60) cc_final: 0.8132 (t60) REVERT: A 818 CYS cc_start: 0.7310 (p) cc_final: 0.7110 (p) REVERT: C 395 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: C 681 MET cc_start: 0.8006 (ptm) cc_final: 0.7781 (ptt) REVERT: C 879 GLU cc_start: 0.8996 (tp30) cc_final: 0.8644 (pt0) REVERT: D 294 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7594 (mmt) REVERT: D 348 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8499 (mp0) REVERT: D 710 ASN cc_start: 0.5609 (t0) cc_final: 0.5331 (m110) REVERT: D 772 TYR cc_start: 0.6914 (m-10) cc_final: 0.6534 (m-10) REVERT: E 667 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7511 (p) REVERT: E 728 MET cc_start: 0.6758 (tpp) cc_final: 0.5748 (ppp) REVERT: E 937 GLU cc_start: 0.5195 (OUTLIER) cc_final: 0.4764 (tp30) REVERT: F 704 ARG cc_start: 0.7630 (mmt-90) cc_final: 0.7298 (tpp80) REVERT: F 732 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7792 (tpt) REVERT: F 801 PHE cc_start: 0.7966 (m-10) cc_final: 0.7136 (m-80) REVERT: G 95 MET cc_start: 0.8403 (tmm) cc_final: 0.7496 (tmm) REVERT: H 708 MET cc_start: 0.7456 (mmm) cc_final: 0.7218 (mmp) REVERT: J 481 MET cc_start: 0.8669 (mmm) cc_final: 0.8272 (mmt) REVERT: K 340 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: K 439 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8360 (tttp) REVERT: M 95 MET cc_start: 0.7898 (tmm) cc_final: 0.7567 (tmm) REVERT: M 248 GLU cc_start: 0.8274 (pm20) cc_final: 0.8010 (mp0) REVERT: M 294 MET cc_start: 0.6170 (mpp) cc_final: 0.5825 (mtm) REVERT: M 598 LEU cc_start: 0.6957 (mt) cc_final: 0.6565 (tp) REVERT: M 631 MET cc_start: 0.6595 (mpp) cc_final: 0.6235 (mtt) REVERT: M 635 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.4821 (mm) outliers start: 99 outliers final: 73 residues processed: 606 average time/residue: 0.6725 time to fit residues: 739.9273 Evaluate side-chains 581 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 500 time to evaluate : 6.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 763 CYS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 871 ASN Chi-restraints excluded: chain D residue 921 TYR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain E residue 937 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 439 LYS Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 732 MET Chi-restraints excluded: chain F residue 782 HIS Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 202 HIS Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 728 MET Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 485 THR Chi-restraints excluded: chain H residue 491 HIS Chi-restraints excluded: chain H residue 612 LEU Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 501 LEU Chi-restraints excluded: chain I residue 583 CYS Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 469 LEU Chi-restraints excluded: chain J residue 551 LEU Chi-restraints excluded: chain J residue 581 HIS Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 247 ILE Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 551 LEU Chi-restraints excluded: chain K residue 614 ILE Chi-restraints excluded: chain K residue 635 LEU Chi-restraints excluded: chain M residue 20 TYR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 217 ASN Chi-restraints excluded: chain M residue 417 MET Chi-restraints excluded: chain M residue 434 VAL Chi-restraints excluded: chain M residue 512 GLU Chi-restraints excluded: chain M residue 635 LEU Chi-restraints excluded: chain M residue 639 CYS Chi-restraints excluded: chain M residue 790 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 626 optimal weight: 3.9990 chunk 404 optimal weight: 1.9990 chunk 605 optimal weight: 2.9990 chunk 305 optimal weight: 0.5980 chunk 199 optimal weight: 0.0870 chunk 196 optimal weight: 6.9990 chunk 644 optimal weight: 5.9990 chunk 690 optimal weight: 8.9990 chunk 500 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 796 optimal weight: 0.7980 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 HIS F 246 ASN G 151 GLN ** H 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 577 HIS ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 81451 Z= 0.190 Angle : 0.496 13.924 110848 Z= 0.255 Chirality : 0.040 0.225 12288 Planarity : 0.003 0.055 14292 Dihedral : 3.719 59.829 11250 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.42 % Allowed : 14.63 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.08), residues: 10347 helix: 2.21 (0.08), residues: 4821 sheet: -0.66 (0.13), residues: 1482 loop : 0.23 (0.10), residues: 4044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 350 HIS 0.008 0.001 HIS I 577 PHE 0.030 0.001 PHE H 801 TYR 0.021 0.001 TYR C 20 ARG 0.006 0.000 ARG H 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 535 time to evaluate : 6.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 634 TRP cc_start: 0.8489 (t60) cc_final: 0.8148 (t60) REVERT: A 818 CYS cc_start: 0.7308 (p) cc_final: 0.7058 (p) REVERT: C 395 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: C 681 MET cc_start: 0.8056 (ptm) cc_final: 0.7845 (ptt) REVERT: C 879 GLU cc_start: 0.8941 (tp30) cc_final: 0.8465 (pt0) REVERT: D 294 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7542 (mmt) REVERT: D 348 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8511 (mp0) REVERT: D 350 TRP cc_start: 0.8031 (t-100) cc_final: 0.7618 (t-100) REVERT: D 690 TYR cc_start: 0.7442 (p90) cc_final: 0.7015 (p90) REVERT: D 710 ASN cc_start: 0.5566 (t0) cc_final: 0.5288 (m110) REVERT: D 772 TYR cc_start: 0.6916 (m-10) cc_final: 0.6566 (m-10) REVERT: E 95 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6730 (tmm) REVERT: E 667 THR cc_start: 0.7702 (OUTLIER) cc_final: 0.7481 (p) REVERT: E 728 MET cc_start: 0.6718 (tpp) cc_final: 0.5786 (ppp) REVERT: E 937 GLU cc_start: 0.5168 (OUTLIER) cc_final: 0.4539 (tp30) REVERT: F 704 ARG cc_start: 0.7613 (mmt-90) cc_final: 0.7282 (tpp80) REVERT: F 801 PHE cc_start: 0.8104 (m-10) cc_final: 0.7571 (m-80) REVERT: G 81 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8662 (pp) REVERT: G 95 MET cc_start: 0.8383 (tmm) cc_final: 0.7504 (tmm) REVERT: H 708 MET cc_start: 0.7451 (mmm) cc_final: 0.7201 (mmp) REVERT: J 208 SER cc_start: 0.7976 (t) cc_final: 0.7735 (t) REVERT: J 294 MET cc_start: 0.7772 (tpp) cc_final: 0.6601 (ptm) REVERT: J 481 MET cc_start: 0.8651 (mmm) cc_final: 0.8285 (mmt) REVERT: K 340 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: K 439 LYS cc_start: 0.8575 (ttpp) cc_final: 0.8352 (tttp) REVERT: M 95 MET cc_start: 0.7951 (tmm) cc_final: 0.7618 (tmm) REVERT: M 248 GLU cc_start: 0.8289 (pm20) cc_final: 0.7934 (mp0) REVERT: M 294 MET cc_start: 0.6217 (mpp) cc_final: 0.5934 (mtm) REVERT: M 598 LEU cc_start: 0.6898 (mt) cc_final: 0.6492 (tp) REVERT: M 631 MET cc_start: 0.6747 (mpp) cc_final: 0.6337 (mtt) REVERT: M 635 LEU cc_start: 0.5060 (OUTLIER) cc_final: 0.4395 (mm) outliers start: 108 outliers final: 79 residues processed: 618 average time/residue: 0.6710 time to fit residues: 743.8734 Evaluate side-chains 596 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 508 time to evaluate : 6.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 763 CYS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 871 ASN Chi-restraints excluded: chain D residue 898 ASN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain E residue 937 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 439 LYS Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 782 HIS Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 202 HIS Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 569 ASN Chi-restraints excluded: chain G residue 843 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 485 THR Chi-restraints excluded: chain H residue 491 HIS Chi-restraints excluded: chain H residue 612 LEU Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 462 LYS Chi-restraints excluded: chain I residue 501 LEU Chi-restraints excluded: chain I residue 583 CYS Chi-restraints excluded: chain I residue 729 THR Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 469 LEU Chi-restraints excluded: chain J residue 551 LEU Chi-restraints excluded: chain J residue 581 HIS Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 247 ILE Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 551 LEU Chi-restraints excluded: chain K residue 614 ILE Chi-restraints excluded: chain K residue 635 LEU Chi-restraints excluded: chain M residue 20 TYR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 217 ASN Chi-restraints excluded: chain M residue 417 MET Chi-restraints excluded: chain M residue 434 VAL Chi-restraints excluded: chain M residue 512 GLU Chi-restraints excluded: chain M residue 635 LEU Chi-restraints excluded: chain M residue 639 CYS Chi-restraints excluded: chain M residue 790 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 921 optimal weight: 0.5980 chunk 970 optimal weight: 4.9990 chunk 885 optimal weight: 3.9990 chunk 943 optimal weight: 9.9990 chunk 568 optimal weight: 0.6980 chunk 411 optimal weight: 4.9990 chunk 741 optimal weight: 0.9980 chunk 289 optimal weight: 1.9990 chunk 853 optimal weight: 20.0000 chunk 892 optimal weight: 3.9990 chunk 940 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 HIS F 246 ASN G 151 GLN G 190 GLN ** H 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 577 HIS ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 81451 Z= 0.157 Angle : 0.491 13.738 110848 Z= 0.250 Chirality : 0.040 0.300 12288 Planarity : 0.003 0.055 14292 Dihedral : 3.599 59.623 11250 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.30 % Allowed : 14.87 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.09), residues: 10347 helix: 2.26 (0.08), residues: 4829 sheet: -0.58 (0.14), residues: 1452 loop : 0.33 (0.10), residues: 4066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 350 HIS 0.008 0.001 HIS I 577 PHE 0.045 0.001 PHE H 801 TYR 0.021 0.001 TYR F 20 ARG 0.007 0.000 ARG H 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 530 time to evaluate : 9.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 634 TRP cc_start: 0.8442 (t60) cc_final: 0.8114 (t60) REVERT: A 818 CYS cc_start: 0.7258 (p) cc_final: 0.7011 (p) REVERT: C 395 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: C 681 MET cc_start: 0.7948 (ptm) cc_final: 0.7748 (ptt) REVERT: C 879 GLU cc_start: 0.8942 (tp30) cc_final: 0.8470 (pt0) REVERT: D 348 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: D 350 TRP cc_start: 0.8011 (t-100) cc_final: 0.7598 (t-100) REVERT: D 690 TYR cc_start: 0.7453 (p90) cc_final: 0.7094 (p90) REVERT: D 710 ASN cc_start: 0.5722 (t0) cc_final: 0.5419 (m110) REVERT: D 772 TYR cc_start: 0.6894 (m-10) cc_final: 0.6578 (m-10) REVERT: D 817 PHE cc_start: 0.7079 (t80) cc_final: 0.6594 (t80) REVERT: D 921 TYR cc_start: 0.3123 (OUTLIER) cc_final: 0.2606 (t80) REVERT: E 95 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6613 (tmm) REVERT: E 667 THR cc_start: 0.7726 (OUTLIER) cc_final: 0.7480 (p) REVERT: E 728 MET cc_start: 0.6746 (tpp) cc_final: 0.5895 (ppp) REVERT: E 937 GLU cc_start: 0.5027 (OUTLIER) cc_final: 0.4211 (tp30) REVERT: F 704 ARG cc_start: 0.7621 (mmt-90) cc_final: 0.7302 (tpp80) REVERT: G 81 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8680 (pp) REVERT: G 95 MET cc_start: 0.8395 (tmm) cc_final: 0.7587 (tmm) REVERT: G 390 TYR cc_start: 0.7218 (t80) cc_final: 0.6923 (t80) REVERT: H 708 MET cc_start: 0.7470 (mmm) cc_final: 0.7232 (mmp) REVERT: J 208 SER cc_start: 0.7923 (t) cc_final: 0.7689 (t) REVERT: K 340 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: M 95 MET cc_start: 0.7922 (tmm) cc_final: 0.7595 (tmm) REVERT: M 248 GLU cc_start: 0.8277 (pm20) cc_final: 0.7907 (mp0) REVERT: M 598 LEU cc_start: 0.6839 (mt) cc_final: 0.6428 (tp) REVERT: M 631 MET cc_start: 0.6837 (mpp) cc_final: 0.6414 (mtt) REVERT: M 635 LEU cc_start: 0.5024 (OUTLIER) cc_final: 0.4382 (mm) REVERT: M 732 MET cc_start: 0.8381 (mmm) cc_final: 0.8014 (mmm) outliers start: 99 outliers final: 79 residues processed: 604 average time/residue: 0.6766 time to fit residues: 736.8907 Evaluate side-chains 605 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 517 time to evaluate : 6.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 763 CYS Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 871 ASN Chi-restraints excluded: chain D residue 898 ASN Chi-restraints excluded: chain D residue 921 TYR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 437 ASN Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain E residue 937 GLU Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 439 LYS Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 782 HIS Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 151 GLN Chi-restraints excluded: chain G residue 202 HIS Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 843 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 485 THR Chi-restraints excluded: chain H residue 491 HIS Chi-restraints excluded: chain H residue 612 LEU Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain I residue 462 LYS Chi-restraints excluded: chain I residue 729 THR Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 469 LEU Chi-restraints excluded: chain J residue 551 LEU Chi-restraints excluded: chain J residue 581 HIS Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 247 ILE Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 551 LEU Chi-restraints excluded: chain K residue 614 ILE Chi-restraints excluded: chain K residue 635 LEU Chi-restraints excluded: chain M residue 20 TYR Chi-restraints excluded: chain M residue 217 ASN Chi-restraints excluded: chain M residue 417 MET Chi-restraints excluded: chain M residue 434 VAL Chi-restraints excluded: chain M residue 512 GLU Chi-restraints excluded: chain M residue 635 LEU Chi-restraints excluded: chain M residue 639 CYS Chi-restraints excluded: chain M residue 790 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 619 optimal weight: 0.0020 chunk 998 optimal weight: 7.9990 chunk 609 optimal weight: 2.9990 chunk 473 optimal weight: 7.9990 chunk 693 optimal weight: 2.9990 chunk 1047 optimal weight: 30.0000 chunk 963 optimal weight: 5.9990 chunk 833 optimal weight: 0.0030 chunk 86 optimal weight: 6.9990 chunk 644 optimal weight: 4.9990 chunk 511 optimal weight: 8.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 HIS C 363 ASN ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 ASN ** H 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 577 HIS ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 450 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 81451 Z= 0.285 Angle : 0.543 12.933 110848 Z= 0.280 Chirality : 0.041 0.303 12288 Planarity : 0.004 0.055 14292 Dihedral : 3.782 58.285 11250 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.76 % Favored : 97.23 % Rotamer: Outliers : 1.34 % Allowed : 15.08 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.09), residues: 10347 helix: 2.15 (0.08), residues: 4828 sheet: -0.70 (0.13), residues: 1497 loop : 0.22 (0.10), residues: 4022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 350 HIS 0.008 0.001 HIS I 577 PHE 0.053 0.002 PHE A 801 TYR 0.022 0.001 TYR K 20 ARG 0.008 0.000 ARG H 479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20694 Ramachandran restraints generated. 10347 Oldfield, 0 Emsley, 10347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 518 time to evaluate : 6.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 818 CYS cc_start: 0.7321 (p) cc_final: 0.7089 (p) REVERT: C 395 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: C 879 GLU cc_start: 0.9006 (tp30) cc_final: 0.8442 (pt0) REVERT: D 348 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8558 (mp0) REVERT: D 350 TRP cc_start: 0.8070 (t-100) cc_final: 0.7751 (t-100) REVERT: D 690 TYR cc_start: 0.7443 (p90) cc_final: 0.7007 (p90) REVERT: D 710 ASN cc_start: 0.5796 (t0) cc_final: 0.5419 (m110) REVERT: D 732 MET cc_start: 0.7385 (mtp) cc_final: 0.6947 (mtp) REVERT: D 772 TYR cc_start: 0.6891 (m-10) cc_final: 0.6541 (m-10) REVERT: D 817 PHE cc_start: 0.7053 (t80) cc_final: 0.6560 (t80) REVERT: E 667 THR cc_start: 0.7736 (OUTLIER) cc_final: 0.7505 (p) REVERT: E 728 MET cc_start: 0.6712 (tpp) cc_final: 0.5933 (ppp) REVERT: E 937 GLU cc_start: 0.5147 (OUTLIER) cc_final: 0.4494 (tp30) REVERT: F 704 ARG cc_start: 0.7630 (mmt-90) cc_final: 0.7326 (tpp80) REVERT: F 741 ILE cc_start: 0.8573 (mm) cc_final: 0.8107 (pt) REVERT: G 81 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8687 (pp) REVERT: G 95 MET cc_start: 0.8400 (tmm) cc_final: 0.7813 (tmm) REVERT: G 486 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: H 691 PHE cc_start: 0.6487 (m-80) cc_final: 0.6245 (m-80) REVERT: H 708 MET cc_start: 0.7510 (mmm) cc_final: 0.7072 (mmm) REVERT: I 425 MET cc_start: 0.8152 (ttm) cc_final: 0.7844 (ttm) REVERT: J 208 SER cc_start: 0.8061 (t) cc_final: 0.7809 (t) REVERT: J 294 MET cc_start: 0.7725 (tpp) cc_final: 0.6612 (ptm) REVERT: K 340 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: M 631 MET cc_start: 0.6888 (mpp) cc_final: 0.6439 (mtt) REVERT: M 635 LEU cc_start: 0.4944 (OUTLIER) cc_final: 0.4187 (mm) REVERT: M 732 MET cc_start: 0.8396 (mmm) cc_final: 0.7994 (mmm) outliers start: 102 outliers final: 87 residues processed: 597 average time/residue: 0.6695 time to fit residues: 719.8811 Evaluate side-chains 600 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 505 time to evaluate : 6.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 763 CYS Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 871 ASN Chi-restraints excluded: chain D residue 898 ASN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain E residue 937 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 439 LYS Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 782 HIS Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 202 HIS Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 569 ASN Chi-restraints excluded: chain G residue 645 LEU Chi-restraints excluded: chain G residue 843 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 485 THR Chi-restraints excluded: chain H residue 491 HIS Chi-restraints excluded: chain H residue 612 LEU Chi-restraints excluded: chain I residue 103 ASN Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 462 LYS Chi-restraints excluded: chain I residue 501 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 469 LEU Chi-restraints excluded: chain J residue 551 LEU Chi-restraints excluded: chain J residue 581 HIS Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 247 ILE Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 551 LEU Chi-restraints excluded: chain K residue 568 ILE Chi-restraints excluded: chain K residue 614 ILE Chi-restraints excluded: chain K residue 635 LEU Chi-restraints excluded: chain M residue 20 TYR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 217 ASN Chi-restraints excluded: chain M residue 417 MET Chi-restraints excluded: chain M residue 434 VAL Chi-restraints excluded: chain M residue 512 GLU Chi-restraints excluded: chain M residue 635 LEU Chi-restraints excluded: chain M residue 639 CYS Chi-restraints excluded: chain M residue 790 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 662 optimal weight: 2.9990 chunk 888 optimal weight: 0.4980 chunk 255 optimal weight: 8.9990 chunk 768 optimal weight: 30.0000 chunk 123 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 835 optimal weight: 4.9990 chunk 349 optimal weight: 7.9990 chunk 857 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 HIS F 246 ASN ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN I 454 GLN I 577 HIS ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.104096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.077002 restraints weight = 306270.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.076703 restraints weight = 195917.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.076413 restraints weight = 157001.636| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 81451 Z= 0.337 Angle : 0.576 15.010 110848 Z= 0.299 Chirality : 0.042 0.357 12288 Planarity : 0.004 0.058 14292 Dihedral : 4.014 56.298 11250 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.62 % Allowed : 14.98 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.08), residues: 10347 helix: 1.95 (0.08), residues: 4827 sheet: -0.83 (0.13), residues: 1478 loop : 0.08 (0.10), residues: 4042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 350 HIS 0.008 0.001 HIS I 577 PHE 0.043 0.002 PHE A 801 TYR 0.023 0.002 TYR K 20 ARG 0.008 0.000 ARG H 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14133.68 seconds wall clock time: 252 minutes 52.45 seconds (15172.45 seconds total)