Starting phenix.real_space_refine on Sun Apr 14 10:39:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vye_43658/04_2024/8vye_43658.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vye_43658/04_2024/8vye_43658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vye_43658/04_2024/8vye_43658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vye_43658/04_2024/8vye_43658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vye_43658/04_2024/8vye_43658.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vye_43658/04_2024/8vye_43658.pdb" } resolution = 2.7 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= 0.004 sd= 0.064 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 138 5.16 5 C 18702 2.51 5 N 5868 2.21 5 O 6432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 571": "OD1" <-> "OD2" Residue "K PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 571": "OD1" <-> "OD2" Residue "E PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 571": "OD1" <-> "OD2" Residue "O PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31140 Number of models: 1 Model: "" Number of chains: 24 Chain: "K" Number of atoms: 7234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 7234 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 248} Link IDs: {'PTRANS': 56, 'TRANS': 979} Chain breaks: 7 Unresolved non-hydrogen bonds: 916 Unresolved non-hydrogen angles: 1161 Unresolved non-hydrogen dihedrals: 763 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 20, 'TYR:plan': 14, 'ASN:plan1': 20, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 16, 'GLU:plan': 25, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 560 Chain: "B" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 494 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 102} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 476 Unresolved non-hydrogen angles: 690 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 267 Chain: "C" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 453 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 90} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 574 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 204 Chain: "A" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 517 Classifications: {'peptide': 126} Incomplete info: {'backbone_only': 105} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 484 Unresolved non-hydrogen angles: 707 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 138 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 261 Chain: "D" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 446 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 87} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 170 Chain: "H" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 525 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 106} Link IDs: {'PTRANS': 7, 'TRANS': 117} Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 677 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 153 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 195 Chain: "L" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 445 Classifications: {'peptide': 105} Incomplete info: {'backbone_only': 85} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 358 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 176 Chain: "E" Number of atoms: 7234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 7234 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 248} Link IDs: {'PTRANS': 56, 'TRANS': 979} Chain breaks: 7 Unresolved non-hydrogen bonds: 916 Unresolved non-hydrogen angles: 1161 Unresolved non-hydrogen dihedrals: 763 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 20, 'TYR:plan': 14, 'ASN:plan1': 20, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 16, 'GLU:plan': 25, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 560 Chain: "F" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 494 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 102} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 476 Unresolved non-hydrogen angles: 690 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 267 Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 453 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 90} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 574 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 204 Chain: "I" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 517 Classifications: {'peptide': 126} Incomplete info: {'backbone_only': 105} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 484 Unresolved non-hydrogen angles: 707 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 138 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 261 Chain: "J" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 446 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 87} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 170 Chain: "M" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 525 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 106} Link IDs: {'PTRANS': 7, 'TRANS': 117} Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 677 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 153 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 195 Chain: "N" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 445 Classifications: {'peptide': 105} Incomplete info: {'backbone_only': 85} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 358 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 176 Chain: "O" Number of atoms: 7234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 7234 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 248} Link IDs: {'PTRANS': 56, 'TRANS': 979} Chain breaks: 7 Unresolved non-hydrogen bonds: 916 Unresolved non-hydrogen angles: 1161 Unresolved non-hydrogen dihedrals: 763 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 20, 'TYR:plan': 14, 'ASN:plan1': 20, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 16, 'GLU:plan': 25, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 560 Chain: "P" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 494 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 102} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 476 Unresolved non-hydrogen angles: 690 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 267 Chain: "Q" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 453 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 90} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 574 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 204 Chain: "R" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 517 Classifications: {'peptide': 126} Incomplete info: {'backbone_only': 105} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 484 Unresolved non-hydrogen angles: 707 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 138 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 261 Chain: "S" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 446 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 87} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 170 Chain: "T" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 525 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 106} Link IDs: {'PTRANS': 7, 'TRANS': 117} Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 677 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 153 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 195 Chain: "U" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 445 Classifications: {'peptide': 105} Incomplete info: {'backbone_only': 85} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 358 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 176 Chain: "K" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 266 Unusual residues: {'NAG': 19} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 19 Chain: "E" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 266 Unusual residues: {'NAG': 19} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 19 Chain: "O" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 266 Unusual residues: {'NAG': 19} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 19 Time building chain proxies: 16.92, per 1000 atoms: 0.54 Number of scatterers: 31140 At special positions: 0 Unit cell: (203.163, 193.89, 190.518, 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 138 16.00 O 6432 8.00 N 5868 7.00 C 18702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 136 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.03 Simple disulfide: pdb=" SG CYS K 284 " - pdb=" SG CYS K 294 " distance=2.02 Simple disulfide: pdb=" SG CYS K 329 " - pdb=" SG CYS K 354 " distance=2.03 Simple disulfide: pdb=" SG CYS K 372 " - pdb=" SG CYS K 425 " distance=2.04 Simple disulfide: pdb=" SG CYS K 384 " - pdb=" SG CYS K 518 " distance=2.12 Simple disulfide: pdb=" SG CYS K 531 " - pdb=" SG CYS K 583 " distance=2.02 Simple disulfide: pdb=" SG CYS K 610 " - pdb=" SG CYS K 642 " distance=2.03 Simple disulfide: pdb=" SG CYS K 655 " - pdb=" SG CYS K 664 " distance=2.04 Simple disulfide: pdb=" SG CYS K 731 " - pdb=" SG CYS K 753 " distance=2.14 Simple disulfide: pdb=" SG CYS K 736 " - pdb=" SG CYS K 742 " distance=2.11 Simple disulfide: pdb=" SG CYS K1025 " - pdb=" SG CYS K1036 " distance=2.02 Simple disulfide: pdb=" SG CYS K1075 " - pdb=" SG CYS K1119 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.02 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.05 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.04 Simple disulfide: pdb=" SG CYS E 284 " - pdb=" SG CYS E 294 " distance=2.02 Simple disulfide: pdb=" SG CYS E 329 " - pdb=" SG CYS E 354 " distance=2.03 Simple disulfide: pdb=" SG CYS E 372 " - pdb=" SG CYS E 425 " distance=2.04 Simple disulfide: pdb=" SG CYS E 384 " - pdb=" SG CYS E 518 " distance=2.12 Simple disulfide: pdb=" SG CYS E 531 " - pdb=" SG CYS E 583 " distance=2.02 Simple disulfide: pdb=" SG CYS E 610 " - pdb=" SG CYS E 642 " distance=2.03 Simple disulfide: pdb=" SG CYS E 655 " - pdb=" SG CYS E 664 " distance=2.04 Simple disulfide: pdb=" SG CYS E 731 " - pdb=" SG CYS E 753 " distance=2.15 Simple disulfide: pdb=" SG CYS E 736 " - pdb=" SG CYS E 742 " distance=2.11 Simple disulfide: pdb=" SG CYS E1025 " - pdb=" SG CYS E1036 " distance=2.02 Simple disulfide: pdb=" SG CYS E1075 " - pdb=" SG CYS E1119 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.05 Simple disulfide: pdb=" SG CYS O 15 " - pdb=" SG CYS O 136 " distance=2.03 Simple disulfide: pdb=" SG CYS O 131 " - pdb=" SG CYS O 166 " distance=2.03 Simple disulfide: pdb=" SG CYS O 284 " - pdb=" SG CYS O 294 " distance=2.02 Simple disulfide: pdb=" SG CYS O 329 " - pdb=" SG CYS O 354 " distance=2.03 Simple disulfide: pdb=" SG CYS O 372 " - pdb=" SG CYS O 425 " distance=2.04 Simple disulfide: pdb=" SG CYS O 384 " - pdb=" SG CYS O 518 " distance=2.12 Simple disulfide: pdb=" SG CYS O 531 " - pdb=" SG CYS O 583 " distance=2.02 Simple disulfide: pdb=" SG CYS O 610 " - pdb=" SG CYS O 642 " distance=2.03 Simple disulfide: pdb=" SG CYS O 655 " - pdb=" SG CYS O 664 " distance=2.04 Simple disulfide: pdb=" SG CYS O 731 " - pdb=" SG CYS O 753 " distance=2.14 Simple disulfide: pdb=" SG CYS O 736 " - pdb=" SG CYS O 742 " distance=2.11 Simple disulfide: pdb=" SG CYS O1025 " - pdb=" SG CYS O1036 " distance=2.02 Simple disulfide: pdb=" SG CYS O1075 " - pdb=" SG CYS O1119 " distance=2.02 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.02 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 89 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E1301 " - " ASN E 324 " " NAG E1302 " - " ASN E 596 " " NAG E1303 " - " ASN E 650 " " NAG E1304 " - " ASN E1067 " " NAG E1305 " - " ASN E1091 " " NAG E1306 " - " ASN E1127 " " NAG E1307 " - " ASN E 609 " " NAG E1308 " - " ASN E 702 " " NAG E1309 " - " ASN E 794 " " NAG E1310 " - " ASN E 710 " " NAG E1311 " - " ASN E 336 " " NAG E1312 " - " ASN E 275 " " NAG E1313 " - " ASN E 122 " " NAG E1314 " - " ASN E 165 " " NAG E1315 " - " ASN E 149 " " NAG E1316 " - " ASN E 17 " " NAG E1317 " - " ASN E 234 " " NAG E1318 " - " ASN E 246 " " NAG E1319 " - " ASN E 61 " " NAG K1301 " - " ASN K 324 " " NAG K1302 " - " ASN K 596 " " NAG K1303 " - " ASN K 650 " " NAG K1304 " - " ASN K1067 " " NAG K1305 " - " ASN K1091 " " NAG K1306 " - " ASN K1127 " " NAG K1307 " - " ASN K 609 " " NAG K1308 " - " ASN K 702 " " NAG K1309 " - " ASN K 794 " " NAG K1310 " - " ASN K 710 " " NAG K1311 " - " ASN K 336 " " NAG K1312 " - " ASN K 275 " " NAG K1313 " - " ASN K 122 " " NAG K1314 " - " ASN K 165 " " NAG K1315 " - " ASN K 149 " " NAG K1316 " - " ASN K 17 " " NAG K1317 " - " ASN K 234 " " NAG K1318 " - " ASN K 246 " " NAG K1319 " - " ASN K 61 " " NAG O1301 " - " ASN O 324 " " NAG O1302 " - " ASN O 596 " " NAG O1303 " - " ASN O 650 " " NAG O1304 " - " ASN O1067 " " NAG O1305 " - " ASN O1091 " " NAG O1306 " - " ASN O1127 " " NAG O1307 " - " ASN O 609 " " NAG O1308 " - " ASN O 702 " " NAG O1309 " - " ASN O 794 " " NAG O1310 " - " ASN O 710 " " NAG O1311 " - " ASN O 336 " " NAG O1312 " - " ASN O 275 " " NAG O1313 " - " ASN O 122 " " NAG O1314 " - " ASN O 165 " " NAG O1315 " - " ASN O 149 " " NAG O1316 " - " ASN O 17 " " NAG O1317 " - " ASN O 234 " " NAG O1318 " - " ASN O 246 " " NAG O1319 " - " ASN O 61 " Time building additional restraints: 12.07 Conformation dependent library (CDL) restraints added in 7.6 seconds 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6096 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 78 sheets defined 18.3% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'K' and resid 287 through 296 Processing helix chain 'K' and resid 331 through 336 Processing helix chain 'K' and resid 342 through 346 removed outlier: 3.663A pdb=" N TRP K 346 " --> pdb=" O VAL K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 363 Processing helix chain 'K' and resid 376 through 382 removed outlier: 4.893A pdb=" N ASN K 381 " --> pdb=" O THR K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 403 removed outlier: 3.910A pdb=" N ARG K 401 " --> pdb=" O ASP K 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 409 through 415 Processing helix chain 'K' and resid 431 through 436 removed outlier: 3.747A pdb=" N SER K 436 " --> pdb=" O ASN K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 495 through 498 Processing helix chain 'K' and resid 609 through 613 Processing helix chain 'K' and resid 730 through 737 Processing helix chain 'K' and resid 739 through 747 removed outlier: 3.519A pdb=" N LEU K 747 " --> pdb=" O SER K 743 " (cutoff:3.500A) Processing helix chain 'K' and resid 748 through 750 No H-bonds generated for 'chain 'K' and resid 748 through 750' Processing helix chain 'K' and resid 751 through 776 removed outlier: 3.894A pdb=" N ASP K 768 " --> pdb=" O ALA K 764 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL K 774 " --> pdb=" O ASN K 770 " (cutoff:3.500A) Processing helix chain 'K' and resid 809 through 819 Processing helix chain 'K' and resid 846 through 849 Processing helix chain 'K' and resid 859 through 878 Processing helix chain 'K' and resid 879 through 883 Processing helix chain 'K' and resid 890 through 901 Processing helix chain 'K' and resid 905 through 911 removed outlier: 4.209A pdb=" N LEU K 909 " --> pdb=" O THR K 905 " (cutoff:3.500A) Processing helix chain 'K' and resid 912 through 933 removed outlier: 3.763A pdb=" N ILE K 927 " --> pdb=" O ALA K 923 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN K 928 " --> pdb=" O ILE K 924 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP K 929 " --> pdb=" O GLY K 925 " (cutoff:3.500A) Processing helix chain 'K' and resid 938 through 958 removed outlier: 3.982A pdb=" N VAL K 944 " --> pdb=" O LYS K 940 " (cutoff:3.500A) Processing helix chain 'K' and resid 959 through 961 No H-bonds generated for 'chain 'K' and resid 959 through 961' Processing helix chain 'K' and resid 969 through 977 Processing helix chain 'K' and resid 978 through 1026 removed outlier: 4.567A pdb=" N VAL K 984 " --> pdb=" O PRO K 980 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG K 988 " --> pdb=" O VAL K 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.883A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'E' and resid 287 through 296 Processing helix chain 'E' and resid 331 through 336 Processing helix chain 'E' and resid 342 through 346 removed outlier: 3.663A pdb=" N TRP E 346 " --> pdb=" O VAL E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 363 Processing helix chain 'E' and resid 376 through 382 removed outlier: 4.893A pdb=" N ASN E 381 " --> pdb=" O THR E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 403 removed outlier: 3.910A pdb=" N ARG E 401 " --> pdb=" O ASP E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 415 Processing helix chain 'E' and resid 431 through 436 removed outlier: 3.746A pdb=" N SER E 436 " --> pdb=" O ASN E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 498 Processing helix chain 'E' and resid 609 through 613 Processing helix chain 'E' and resid 730 through 737 Processing helix chain 'E' and resid 739 through 747 removed outlier: 3.519A pdb=" N LEU E 747 " --> pdb=" O SER E 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 750 No H-bonds generated for 'chain 'E' and resid 748 through 750' Processing helix chain 'E' and resid 751 through 776 removed outlier: 3.894A pdb=" N ASP E 768 " --> pdb=" O ALA E 764 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 774 " --> pdb=" O ASN E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 819 Processing helix chain 'E' and resid 846 through 849 Processing helix chain 'E' and resid 859 through 878 Processing helix chain 'E' and resid 879 through 883 Processing helix chain 'E' and resid 890 through 901 Processing helix chain 'E' and resid 905 through 911 removed outlier: 4.209A pdb=" N LEU E 909 " --> pdb=" O THR E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 933 removed outlier: 3.763A pdb=" N ILE E 927 " --> pdb=" O ALA E 923 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN E 928 " --> pdb=" O ILE E 924 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP E 929 " --> pdb=" O GLY E 925 " (cutoff:3.500A) Processing helix chain 'E' and resid 938 through 958 removed outlier: 3.982A pdb=" N VAL E 944 " --> pdb=" O LYS E 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 959 through 961 No H-bonds generated for 'chain 'E' and resid 959 through 961' Processing helix chain 'E' and resid 969 through 977 Processing helix chain 'E' and resid 978 through 1026 removed outlier: 4.567A pdb=" N VAL E 984 " --> pdb=" O PRO E 980 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG E 988 " --> pdb=" O VAL E 984 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.882A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'M' and resid 65 through 67 No H-bonds generated for 'chain 'M' and resid 65 through 67' Processing helix chain 'M' and resid 88 through 92 Processing helix chain 'N' and resid 26 through 30 Processing helix chain 'N' and resid 78 through 82 Processing helix chain 'O' and resid 287 through 296 Processing helix chain 'O' and resid 331 through 336 Processing helix chain 'O' and resid 342 through 346 removed outlier: 3.664A pdb=" N TRP O 346 " --> pdb=" O VAL O 343 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 363 Processing helix chain 'O' and resid 376 through 382 removed outlier: 4.893A pdb=" N ASN O 381 " --> pdb=" O THR O 378 " (cutoff:3.500A) Processing helix chain 'O' and resid 398 through 403 removed outlier: 3.909A pdb=" N ARG O 401 " --> pdb=" O ASP O 398 " (cutoff:3.500A) Processing helix chain 'O' and resid 409 through 415 Processing helix chain 'O' and resid 431 through 436 removed outlier: 3.747A pdb=" N SER O 436 " --> pdb=" O ASN O 432 " (cutoff:3.500A) Processing helix chain 'O' and resid 495 through 498 Processing helix chain 'O' and resid 609 through 613 Processing helix chain 'O' and resid 730 through 737 Processing helix chain 'O' and resid 739 through 747 removed outlier: 3.519A pdb=" N LEU O 747 " --> pdb=" O SER O 743 " (cutoff:3.500A) Processing helix chain 'O' and resid 748 through 750 No H-bonds generated for 'chain 'O' and resid 748 through 750' Processing helix chain 'O' and resid 751 through 776 removed outlier: 3.894A pdb=" N ASP O 768 " --> pdb=" O ALA O 764 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL O 774 " --> pdb=" O ASN O 770 " (cutoff:3.500A) Processing helix chain 'O' and resid 809 through 819 Processing helix chain 'O' and resid 846 through 849 Processing helix chain 'O' and resid 859 through 878 Processing helix chain 'O' and resid 879 through 883 Processing helix chain 'O' and resid 890 through 901 Processing helix chain 'O' and resid 905 through 911 removed outlier: 4.210A pdb=" N LEU O 909 " --> pdb=" O THR O 905 " (cutoff:3.500A) Processing helix chain 'O' and resid 912 through 933 removed outlier: 3.763A pdb=" N ILE O 927 " --> pdb=" O ALA O 923 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN O 928 " --> pdb=" O ILE O 924 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP O 929 " --> pdb=" O GLY O 925 " (cutoff:3.500A) Processing helix chain 'O' and resid 938 through 958 removed outlier: 3.982A pdb=" N VAL O 944 " --> pdb=" O LYS O 940 " (cutoff:3.500A) Processing helix chain 'O' and resid 959 through 961 No H-bonds generated for 'chain 'O' and resid 959 through 961' Processing helix chain 'O' and resid 969 through 977 Processing helix chain 'O' and resid 978 through 1026 removed outlier: 4.567A pdb=" N VAL O 984 " --> pdb=" O PRO O 980 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG O 988 " --> pdb=" O VAL O 984 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 87 through 91 Processing helix chain 'R' and resid 28 through 32 removed outlier: 3.882A pdb=" N TYR R 32 " --> pdb=" O PHE R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'S' and resid 30 through 32 No H-bonds generated for 'chain 'S' and resid 30 through 32' Processing helix chain 'T' and resid 65 through 67 No H-bonds generated for 'chain 'T' and resid 65 through 67' Processing helix chain 'T' and resid 88 through 92 Processing helix chain 'U' and resid 26 through 30 Processing helix chain 'U' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain 'K' and resid 28 through 30 removed outlier: 8.398A pdb=" N ASN K 61 " --> pdb=" O TYR K 262 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR K 262 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA K 257 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR K 95 " --> pdb=" O ALA K 257 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN K 188 " --> pdb=" O GLU K 96 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N HIS K 207 " --> pdb=" O ALA K 222 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N ALA K 222 " --> pdb=" O HIS K 207 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL K 36 " --> pdb=" O LEU K 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 47 through 55 removed outlier: 3.753A pdb=" N ASP K 280 " --> pdb=" O LYS K 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 84 through 85 current: chain 'K' and resid 116 through 121 removed outlier: 11.357A pdb=" N VAL K 126 " --> pdb=" O GLU K 169 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N GLU K 169 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 11.400A pdb=" N ILE K 128 " --> pdb=" O THR K 167 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N THR K 167 " --> pdb=" O ILE K 128 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL K 130 " --> pdb=" O ASN K 165 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN K 165 " --> pdb=" O VAL K 130 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLU K 132 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA K 163 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN K 134 " --> pdb=" O SER K 161 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL K 159 " --> pdb=" O CYS K 136 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N ASP K 138 " --> pdb=" O PHE K 157 " (cutoff:3.500A) removed outlier: 10.974A pdb=" N PHE K 157 " --> pdb=" O ASP K 138 " (cutoff:3.500A) removed outlier: 12.480A pdb=" N PHE K 140 " --> pdb=" O SER K 155 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N SER K 155 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLY K 142 " --> pdb=" O MET K 153 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N MET K 153 " --> pdb=" O GLY K 142 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 152 through 172 current: chain 'K' and resid 250 through 252 Processing sheet with id=AA4, first strand: chain 'K' and resid 304 through 312 removed outlier: 7.006A pdb=" N VAL K 588 " --> pdb=" O THR K 308 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN K 310 " --> pdb=" O GLY K 586 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY K 586 " --> pdb=" O ASN K 310 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY K 587 " --> pdb=" O GLN K 606 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 317 through 318 removed outlier: 6.688A pdb=" N GLU K 317 " --> pdb=" O ASN K 533 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ASN K 535 " --> pdb=" O GLU K 317 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP K 567 " --> pdb=" O ILE K 580 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA K 568 " --> pdb=" O GLY K 559 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 347 through 351 Processing sheet with id=AA7, first strand: chain 'K' and resid 354 through 355 removed outlier: 6.583A pdb=" N CYS K 354 " --> pdb=" O CYS K 518 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 445 through 447 Processing sheet with id=AA9, first strand: chain 'K' and resid 647 through 648 removed outlier: 6.603A pdb=" N ILE K 663 " --> pdb=" O ILE K 659 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 695 through 697 removed outlier: 3.831A pdb=" N LYS O 783 " --> pdb=" O ASN K 696 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 704 through 721 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 704 through 721 current: chain 'K' and resid 1052 through 1071 removed outlier: 3.746A pdb=" N ALA K1071 " --> pdb=" O PHE K1088 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE K1088 " --> pdb=" O ALA K1071 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 726 through 729 removed outlier: 4.347A pdb=" N LYS K 726 " --> pdb=" O LEU K 854 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 781 through 783 removed outlier: 5.738A pdb=" N ILE K 781 " --> pdb=" O ASN E 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'K' and resid 1113 through 1118 removed outlier: 4.729A pdb=" N ALA K1080 " --> pdb=" O SER K1116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'B' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 11 through 12 current: chain 'B' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 60 current: chain 'B' and resid 111 through 112 Processing sheet with id=AB8, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'C' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 13 current: chain 'C' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 53 through 54 current: chain 'C' and resid 97 through 98 Processing sheet with id=AC1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'A' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 10 through 12 current: chain 'A' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 60 current: chain 'A' and resid 114 through 115 Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 12 current: chain 'D' and resid 46 through 50 removed outlier: 3.526A pdb=" N SER D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 55 current: chain 'D' and resid 97 through 98 Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.230A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 102 through 103 removed outlier: 4.169A pdb=" N LEU H 108 " --> pdb=" O TRP H 103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 9 through 11 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 11 current: chain 'L' and resid 44 through 47 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 44 through 47 current: chain 'L' and resid 94 through 97 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AD1, first strand: chain 'E' and resid 28 through 30 removed outlier: 8.398A pdb=" N ASN E 61 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR E 262 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA E 257 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR E 95 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN E 188 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 47 through 55 removed outlier: 3.753A pdb=" N ASP E 280 " --> pdb=" O LYS E 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 84 through 85 current: chain 'E' and resid 116 through 121 removed outlier: 11.357A pdb=" N VAL E 126 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N GLU E 169 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 11.399A pdb=" N ILE E 128 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N THR E 167 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL E 130 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN E 165 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLU E 132 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA E 163 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN E 134 " --> pdb=" O SER E 161 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL E 159 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N ASP E 138 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 10.973A pdb=" N PHE E 157 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 12.480A pdb=" N PHE E 140 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N SER E 155 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLY E 142 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET E 153 " --> pdb=" O GLY E 142 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 152 through 172 current: chain 'E' and resid 250 through 252 Processing sheet with id=AD4, first strand: chain 'E' and resid 304 through 312 removed outlier: 7.006A pdb=" N VAL E 588 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASN E 310 " --> pdb=" O GLY E 586 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY E 586 " --> pdb=" O ASN E 310 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY E 587 " --> pdb=" O GLN E 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 317 through 318 removed outlier: 6.689A pdb=" N GLU E 317 " --> pdb=" O ASN E 533 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ASN E 535 " --> pdb=" O GLU E 317 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP E 567 " --> pdb=" O ILE E 580 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA E 568 " --> pdb=" O GLY E 559 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 347 through 351 Processing sheet with id=AD7, first strand: chain 'E' and resid 354 through 355 removed outlier: 6.583A pdb=" N CYS E 354 " --> pdb=" O CYS E 518 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 445 through 447 Processing sheet with id=AD9, first strand: chain 'E' and resid 647 through 648 removed outlier: 6.603A pdb=" N ILE E 663 " --> pdb=" O ILE E 659 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 704 through 721 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 704 through 721 current: chain 'E' and resid 1052 through 1071 removed outlier: 3.745A pdb=" N ALA E1071 " --> pdb=" O PHE E1088 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE E1088 " --> pdb=" O ALA E1071 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 726 through 729 removed outlier: 4.347A pdb=" N LYS E 726 " --> pdb=" O LEU E 854 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 781 through 783 removed outlier: 5.738A pdb=" N ILE E 781 " --> pdb=" O ASN O 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 1113 through 1118 removed outlier: 4.730A pdb=" N ALA E1080 " --> pdb=" O SER E1116 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'F' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 11 through 12 current: chain 'F' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 58 through 60 current: chain 'F' and resid 111 through 112 Processing sheet with id=AE7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'G' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 13 current: chain 'G' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 53 through 54 current: chain 'G' and resid 97 through 98 Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'I' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 10 through 12 current: chain 'I' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 58 through 60 current: chain 'I' and resid 114 through 115 Processing sheet with id=AF2, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 46 through 50 removed outlier: 3.526A pdb=" N SER J 54 " --> pdb=" O TYR J 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 54 through 55 current: chain 'J' and resid 97 through 98 Processing sheet with id=AF4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.230A pdb=" N ARG M 40 " --> pdb=" O TRP M 49 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TRP M 49 " --> pdb=" O ARG M 40 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 102 through 103 removed outlier: 4.169A pdb=" N LEU M 108 " --> pdb=" O TRP M 103 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 9 through 11 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 9 through 11 current: chain 'N' and resid 44 through 47 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 44 through 47 current: chain 'N' and resid 94 through 97 No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AF9, first strand: chain 'O' and resid 28 through 30 removed outlier: 8.398A pdb=" N ASN O 61 " --> pdb=" O TYR O 262 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR O 262 " --> pdb=" O ASN O 61 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA O 257 " --> pdb=" O THR O 95 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR O 95 " --> pdb=" O ALA O 257 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN O 188 " --> pdb=" O GLU O 96 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE O 201 " --> pdb=" O ASP O 228 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP O 228 " --> pdb=" O PHE O 201 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE O 203 " --> pdb=" O LEU O 226 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N HIS O 207 " --> pdb=" O ALA O 222 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ALA O 222 " --> pdb=" O HIS O 207 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL O 36 " --> pdb=" O LEU O 223 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 47 through 55 removed outlier: 3.753A pdb=" N ASP O 280 " --> pdb=" O LYS O 271 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 84 through 85 current: chain 'O' and resid 116 through 121 removed outlier: 11.357A pdb=" N VAL O 126 " --> pdb=" O GLU O 169 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N GLU O 169 " --> pdb=" O VAL O 126 " (cutoff:3.500A) removed outlier: 11.399A pdb=" N ILE O 128 " --> pdb=" O THR O 167 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N THR O 167 " --> pdb=" O ILE O 128 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL O 130 " --> pdb=" O ASN O 165 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN O 165 " --> pdb=" O VAL O 130 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU O 132 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA O 163 " --> pdb=" O GLU O 132 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN O 134 " --> pdb=" O SER O 161 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL O 159 " --> pdb=" O CYS O 136 " (cutoff:3.500A) removed outlier: 11.368A pdb=" N ASP O 138 " --> pdb=" O PHE O 157 " (cutoff:3.500A) removed outlier: 10.974A pdb=" N PHE O 157 " --> pdb=" O ASP O 138 " (cutoff:3.500A) removed outlier: 12.479A pdb=" N PHE O 140 " --> pdb=" O SER O 155 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N SER O 155 " --> pdb=" O PHE O 140 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLY O 142 " --> pdb=" O MET O 153 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N MET O 153 " --> pdb=" O GLY O 142 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 152 through 172 current: chain 'O' and resid 250 through 252 Processing sheet with id=AG3, first strand: chain 'O' and resid 304 through 312 removed outlier: 7.006A pdb=" N VAL O 588 " --> pdb=" O THR O 308 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN O 310 " --> pdb=" O GLY O 586 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY O 586 " --> pdb=" O ASN O 310 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY O 587 " --> pdb=" O GLN O 606 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 317 through 318 removed outlier: 6.689A pdb=" N GLU O 317 " --> pdb=" O ASN O 533 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ASN O 535 " --> pdb=" O GLU O 317 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP O 567 " --> pdb=" O ILE O 580 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA O 568 " --> pdb=" O GLY O 559 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 347 through 351 Processing sheet with id=AG6, first strand: chain 'O' and resid 354 through 355 removed outlier: 6.583A pdb=" N CYS O 354 " --> pdb=" O CYS O 518 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 445 through 447 Processing sheet with id=AG8, first strand: chain 'O' and resid 647 through 648 removed outlier: 6.603A pdb=" N ILE O 663 " --> pdb=" O ILE O 659 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 704 through 721 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 704 through 721 current: chain 'O' and resid 1052 through 1071 removed outlier: 3.745A pdb=" N ALA O1071 " --> pdb=" O PHE O1088 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE O1088 " --> pdb=" O ALA O1071 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 726 through 729 removed outlier: 4.348A pdb=" N LYS O 726 " --> pdb=" O LEU O 854 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'O' and resid 1113 through 1118 removed outlier: 4.729A pdb=" N ALA O1080 " --> pdb=" O SER O1116 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AH4, first strand: chain 'P' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 11 through 12 current: chain 'P' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 58 through 60 current: chain 'P' and resid 111 through 112 Processing sheet with id=AH5, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AH6, first strand: chain 'Q' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 10 through 13 current: chain 'Q' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 53 through 54 current: chain 'Q' and resid 97 through 98 Processing sheet with id=AH7, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=AH8, first strand: chain 'R' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 10 through 12 current: chain 'R' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 58 through 60 current: chain 'R' and resid 114 through 115 Processing sheet with id=AH9, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AI1, first strand: chain 'S' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 10 through 12 current: chain 'S' and resid 46 through 50 removed outlier: 3.525A pdb=" N SER S 54 " --> pdb=" O TYR S 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 54 through 55 current: chain 'S' and resid 97 through 98 Processing sheet with id=AI2, first strand: chain 'T' and resid 3 through 7 Processing sheet with id=AI3, first strand: chain 'T' and resid 11 through 12 removed outlier: 6.230A pdb=" N ARG T 40 " --> pdb=" O TRP T 49 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TRP T 49 " --> pdb=" O ARG T 40 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'T' and resid 102 through 103 removed outlier: 4.169A pdb=" N LEU T 108 " --> pdb=" O TRP T 103 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'U' and resid 9 through 11 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 9 through 11 current: chain 'U' and resid 44 through 47 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 44 through 47 current: chain 'U' and resid 94 through 97 No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'U' and resid 18 through 23 1333 hydrogen bonds defined for protein. 3423 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: 18.78 Time building geometry restraints manager: 13.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9801 1.33 - 1.46: 6052 1.46 - 1.58: 15668 1.58 - 1.71: 0 1.71 - 1.84: 162 Bond restraints: 31683 Sorted by residual: bond pdb=" N VAL E 143 " pdb=" CA VAL E 143 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.11e-02 8.12e+03 9.65e+00 bond pdb=" CA PRO K 979 " pdb=" C PRO K 979 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.58e+00 bond pdb=" N VAL O 143 " pdb=" CA VAL O 143 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.11e-02 8.12e+03 9.55e+00 bond pdb=" CA PRO E 979 " pdb=" C PRO E 979 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.53e+00 bond pdb=" CA PRO O 979 " pdb=" C PRO O 979 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.42e+00 ... (remaining 31678 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.10: 1102 106.10 - 113.03: 14681 113.03 - 119.96: 9087 119.96 - 126.89: 17537 126.89 - 133.82: 181 Bond angle restraints: 42588 Sorted by residual: angle pdb=" C GLN U 6 " pdb=" N PRO U 7 " pdb=" CA PRO U 7 " ideal model delta sigma weight residual 119.66 126.75 -7.09 7.30e-01 1.88e+00 9.43e+01 angle pdb=" C GLN N 6 " pdb=" N PRO N 7 " pdb=" CA PRO N 7 " ideal model delta sigma weight residual 119.66 126.74 -7.08 7.30e-01 1.88e+00 9.41e+01 angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 126.72 -7.06 7.30e-01 1.88e+00 9.34e+01 angle pdb=" C LEU K 854 " pdb=" N PRO K 855 " pdb=" CA PRO K 855 " ideal model delta sigma weight residual 119.66 126.51 -6.85 7.20e-01 1.93e+00 9.05e+01 angle pdb=" C LEU E 854 " pdb=" N PRO E 855 " pdb=" CA PRO E 855 " ideal model delta sigma weight residual 119.66 126.51 -6.85 7.20e-01 1.93e+00 9.04e+01 ... (remaining 42583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 16529 17.64 - 35.27: 334 35.27 - 52.91: 87 52.91 - 70.55: 42 70.55 - 88.19: 9 Dihedral angle restraints: 17001 sinusoidal: 5676 harmonic: 11325 Sorted by residual: dihedral pdb=" CB CYS P 22 " pdb=" SG CYS P 22 " pdb=" SG CYS P 96 " pdb=" CB CYS P 96 " ideal model delta sinusoidal sigma weight residual 93.00 46.48 46.52 1 1.00e+01 1.00e-02 2.99e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 46.50 46.50 1 1.00e+01 1.00e-02 2.99e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 96 " pdb=" CB CYS F 96 " ideal model delta sinusoidal sigma weight residual 93.00 46.54 46.46 1 1.00e+01 1.00e-02 2.99e+01 ... (remaining 16998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3054 0.070 - 0.141: 711 0.141 - 0.211: 201 0.211 - 0.281: 54 0.281 - 0.352: 33 Chirality restraints: 4053 Sorted by residual: chirality pdb=" C2 NAG O1304 " pdb=" C1 NAG O1304 " pdb=" C3 NAG O1304 " pdb=" N2 NAG O1304 " both_signs ideal model delta sigma weight residual False -2.49 -2.84 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C2 NAG E1304 " pdb=" C1 NAG E1304 " pdb=" C3 NAG E1304 " pdb=" N2 NAG E1304 " both_signs ideal model delta sigma weight residual False -2.49 -2.84 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C2 NAG K1304 " pdb=" C1 NAG K1304 " pdb=" C3 NAG K1304 " pdb=" N2 NAG K1304 " both_signs ideal model delta sigma weight residual False -2.49 -2.84 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 4050 not shown) Planarity restraints: 6294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 61 " 0.040 2.00e-02 2.50e+03 4.03e-02 2.03e+01 pdb=" CG ASN K 61 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN K 61 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN K 61 " -0.060 2.00e-02 2.50e+03 pdb=" C1 NAG K1319 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN O 61 " -0.040 2.00e-02 2.50e+03 4.03e-02 2.03e+01 pdb=" CG ASN O 61 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN O 61 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN O 61 " 0.060 2.00e-02 2.50e+03 pdb=" C1 NAG O1319 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 61 " 0.040 2.00e-02 2.50e+03 4.02e-02 2.02e+01 pdb=" CG ASN E 61 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN E 61 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN E 61 " -0.060 2.00e-02 2.50e+03 pdb=" C1 NAG E1319 " 0.048 2.00e-02 2.50e+03 ... (remaining 6291 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 13256 2.90 - 3.40: 23987 3.40 - 3.90: 46201 3.90 - 4.40: 49822 4.40 - 4.90: 85288 Nonbonded interactions: 218554 Sorted by model distance: nonbonded pdb=" O THR O 95 " pdb=" OG1 THR O 95 " model vdw 2.401 2.440 nonbonded pdb=" O THR E 95 " pdb=" OG1 THR E 95 " model vdw 2.401 2.440 nonbonded pdb=" O THR K 95 " pdb=" OG1 THR K 95 " model vdw 2.401 2.440 nonbonded pdb=" OD2 ASP O 111 " pdb=" NZ LYS O 113 " model vdw 2.404 2.520 nonbonded pdb=" OD2 ASP E 111 " pdb=" NZ LYS E 113 " model vdw 2.404 2.520 ... (remaining 218549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' selection = chain 'R' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'S' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'T' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.630 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 28.410 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 91.670 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.380 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:14.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 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 : 0.009 0.059 31683 Z= 0.622 Angle : 1.310 8.229 42588 Z= 0.897 Chirality : 0.075 0.352 4053 Planarity : 0.005 0.022 6237 Dihedral : 8.857 88.187 10752 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.11), residues: 5094 helix: 0.36 (0.19), residues: 666 sheet: 1.12 (0.12), residues: 1644 loop : 0.29 (0.11), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.005 TRP K 879 HIS 0.002 0.001 HIS K 648 PHE 0.019 0.003 PHE K 891 TYR 0.033 0.004 TYR K1060 ARG 0.003 0.000 ARG E1012 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 3.946 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 1.2339 time to fit residues: 539.9836 Evaluate side-chains 195 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 428 optimal weight: 0.6980 chunk 384 optimal weight: 40.0000 chunk 213 optimal weight: 8.9990 chunk 131 optimal weight: 0.0470 chunk 259 optimal weight: 0.5980 chunk 205 optimal weight: 30.0000 chunk 397 optimal weight: 0.7980 chunk 153 optimal weight: 0.0980 chunk 241 optimal weight: 0.7980 chunk 295 optimal weight: 40.0000 chunk 460 optimal weight: 10.0000 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 634 ASN K 894 GLN K1118 ASN E 121 ASN E 651 ASN E 894 GLN E 928 GLN O 30 ASN O 648 HIS O 651 ASN O 748 GLN O 894 GLN O1118 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31683 Z= 0.152 Angle : 0.522 10.168 42588 Z= 0.271 Chirality : 0.047 0.404 4053 Planarity : 0.004 0.039 6237 Dihedral : 4.472 55.188 6486 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.46 % Allowed : 5.10 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 1.36 (0.12), residues: 5094 helix: 2.15 (0.21), residues: 618 sheet: 1.05 (0.12), residues: 1719 loop : 0.65 (0.12), residues: 2757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 879 HIS 0.008 0.001 HIS E 648 PHE 0.016 0.001 PHE K 192 TYR 0.017 0.001 TYR E 258 ARG 0.008 0.001 ARG K 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 230 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 202 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7508 (mmpt) REVERT: K 733 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6308 (tmm) REVERT: E 202 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7439 (mmpt) REVERT: E 307 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: E 733 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6200 (tmm) REVERT: E 748 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7280 (mt0) REVERT: O 202 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7467 (mmpt) REVERT: O 307 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: O 733 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6426 (tmm) outliers start: 52 outliers final: 19 residues processed: 256 average time/residue: 1.1621 time to fit residues: 364.7592 Evaluate side-chains 232 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 204 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain K residue 569 VAL Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 609 ASN Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 740 THR Chi-restraints excluded: chain K residue 744 ASN Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 609 ASN Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain E residue 733 MET Chi-restraints excluded: chain E residue 748 GLN Chi-restraints excluded: chain O residue 202 LYS Chi-restraints excluded: chain O residue 298 SER Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 584 SER Chi-restraints excluded: chain O residue 609 ASN Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 977 LEU Chi-restraints excluded: chain O residue 1003 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 255 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 383 optimal weight: 0.9980 chunk 313 optimal weight: 50.0000 chunk 127 optimal weight: 50.0000 chunk 461 optimal weight: 20.0000 chunk 498 optimal weight: 6.9990 chunk 410 optimal weight: 0.7980 chunk 457 optimal weight: 0.0050 chunk 157 optimal weight: 50.0000 chunk 370 optimal weight: 8.9990 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 648 HIS E 648 HIS O 121 ASN O 748 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 31683 Z= 0.361 Angle : 0.607 10.227 42588 Z= 0.313 Chirality : 0.053 0.438 4053 Planarity : 0.005 0.044 6237 Dihedral : 4.621 52.433 6486 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.97 % Allowed : 6.66 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 1.19 (0.12), residues: 5094 helix: 1.44 (0.20), residues: 642 sheet: 1.02 (0.12), residues: 1788 loop : 0.60 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 879 HIS 0.008 0.002 HIS E 648 PHE 0.023 0.003 PHE E 816 TYR 0.024 0.002 TYR E 258 ARG 0.007 0.001 ARG O1100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 213 time to evaluate : 3.826 Fit side-chains REVERT: K 52 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: K 733 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6434 (tmm) REVERT: K 950 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6848 (mt0) REVERT: E 202 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7595 (mmpt) REVERT: E 229 LEU cc_start: 0.6429 (mt) cc_final: 0.6150 (mt) REVERT: E 307 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: E 733 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6423 (tmm) REVERT: E 748 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7297 (mt0) REVERT: O 307 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: O 532 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7817 (m) REVERT: O 733 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6539 (tmm) REVERT: O 950 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6729 (mt0) outliers start: 63 outliers final: 30 residues processed: 248 average time/residue: 1.0926 time to fit residues: 337.6473 Evaluate side-chains 240 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 532 VAL Chi-restraints excluded: chain K residue 569 VAL Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 608 VAL Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 744 ASN Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 909 LEU Chi-restraints excluded: chain K residue 950 GLN Chi-restraints excluded: chain K residue 969 VAL Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 733 MET Chi-restraints excluded: chain E residue 748 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1003 GLN Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 575 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 584 SER Chi-restraints excluded: chain O residue 608 VAL Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 950 GLN Chi-restraints excluded: chain O residue 977 LEU Chi-restraints excluded: chain O residue 998 GLN Chi-restraints excluded: chain O residue 1010 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 455 optimal weight: 0.0470 chunk 346 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 309 optimal weight: 50.0000 chunk 462 optimal weight: 30.0000 chunk 490 optimal weight: 50.0000 chunk 241 optimal weight: 0.9980 chunk 438 optimal weight: 0.0670 chunk 132 optimal weight: 50.0000 overall best weight: 0.9818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 606 GLN E1003 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31683 Z= 0.200 Angle : 0.512 10.226 42588 Z= 0.260 Chirality : 0.049 0.697 4053 Planarity : 0.004 0.039 6237 Dihedral : 4.364 59.915 6486 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.07 % Allowed : 6.75 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 1.31 (0.12), residues: 5094 helix: 1.81 (0.21), residues: 630 sheet: 1.06 (0.12), residues: 1779 loop : 0.64 (0.12), residues: 2685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 879 HIS 0.003 0.001 HIS E1051 PHE 0.015 0.002 PHE O1114 TYR 0.016 0.002 TYR O 258 ARG 0.006 0.001 ARG O 570 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 215 time to evaluate : 3.837 Fit side-chains REVERT: K 52 GLN cc_start: 0.7186 (tm-30) cc_final: 0.6865 (tm-30) REVERT: K 81 ASN cc_start: 0.5891 (p0) cc_final: 0.5610 (p0) REVERT: K 202 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7894 (mtmt) REVERT: K 570 ARG cc_start: 0.6764 (ttm170) cc_final: 0.6362 (ttm170) REVERT: K 733 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6320 (tmm) REVERT: E 202 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7596 (mmpt) REVERT: E 307 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: E 748 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7288 (mm-40) REVERT: E 998 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: O 202 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7565 (mmpt) REVERT: O 307 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: O 532 VAL cc_start: 0.7995 (p) cc_final: 0.7735 (m) REVERT: O 570 ARG cc_start: 0.6700 (ttm-80) cc_final: 0.6456 (ttm170) REVERT: O 733 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6450 (tmm) outliers start: 65 outliers final: 32 residues processed: 254 average time/residue: 1.1417 time to fit residues: 359.4475 Evaluate side-chains 247 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain K residue 569 VAL Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 608 VAL Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 744 ASN Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 909 LEU Chi-restraints excluded: chain K residue 969 VAL Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 748 GLN Chi-restraints excluded: chain E residue 998 GLN Chi-restraints excluded: chain E residue 1003 GLN Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 202 LYS Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 298 SER Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 584 SER Chi-restraints excluded: chain O residue 608 VAL Chi-restraints excluded: chain O residue 695 GLU Chi-restraints excluded: chain O residue 712 THR Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 977 LEU Chi-restraints excluded: chain O residue 995 GLN Chi-restraints excluded: chain O residue 998 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 408 optimal weight: 0.0010 chunk 278 optimal weight: 50.0000 chunk 7 optimal weight: 3.9990 chunk 364 optimal weight: 0.9990 chunk 202 optimal weight: 10.0000 chunk 418 optimal weight: 0.9990 chunk 338 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 250 optimal weight: 0.9980 chunk 439 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 537 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31683 Z= 0.174 Angle : 0.497 10.137 42588 Z= 0.251 Chirality : 0.048 0.587 4053 Planarity : 0.004 0.044 6237 Dihedral : 4.333 56.558 6486 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.74 % Allowed : 7.32 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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 (0.12), residues: 5094 helix: 2.04 (0.21), residues: 621 sheet: 1.16 (0.12), residues: 1779 loop : 0.65 (0.12), residues: 2694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 879 HIS 0.003 0.001 HIS E1051 PHE 0.018 0.001 PHE E 65 TYR 0.017 0.001 TYR E 653 ARG 0.009 0.001 ARG K 976 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 210 time to evaluate : 3.671 Fit side-chains REVERT: K 52 GLN cc_start: 0.7135 (tm-30) cc_final: 0.6800 (tm-30) REVERT: K 81 ASN cc_start: 0.5911 (p0) cc_final: 0.5707 (p0) REVERT: K 733 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.6342 (tmm) REVERT: E 202 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7617 (mmpt) REVERT: E 307 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: E 748 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7268 (mm-40) REVERT: E 998 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7398 (tt0) REVERT: O 81 ASN cc_start: 0.6277 (p0) cc_final: 0.6026 (p0) REVERT: O 202 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7551 (mmpt) REVERT: O 307 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: O 532 VAL cc_start: 0.7985 (p) cc_final: 0.7716 (m) REVERT: O 733 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6475 (tmm) REVERT: O 950 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6736 (mt0) outliers start: 58 outliers final: 29 residues processed: 240 average time/residue: 1.1171 time to fit residues: 331.5191 Evaluate side-chains 242 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 537 ASN Chi-restraints excluded: chain K residue 569 VAL Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 744 ASN Chi-restraints excluded: chain K residue 784 THR Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 969 VAL Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 748 GLN Chi-restraints excluded: chain E residue 998 GLN Chi-restraints excluded: chain O residue 202 LYS Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 575 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 584 SER Chi-restraints excluded: chain O residue 712 THR Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 895 MET Chi-restraints excluded: chain O residue 950 GLN Chi-restraints excluded: chain O residue 977 LEU Chi-restraints excluded: chain O residue 995 GLN Chi-restraints excluded: chain O residue 998 GLN Chi-restraints excluded: chain O residue 1010 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 164 optimal weight: 40.0000 chunk 441 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 287 optimal weight: 9.9990 chunk 120 optimal weight: 40.0000 chunk 490 optimal weight: 50.0000 chunk 407 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 257 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 66 HIS K 537 ASN K1128 ASN E 634 ASN O 66 HIS O1128 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 31683 Z= 0.447 Angle : 0.648 12.512 42588 Z= 0.329 Chirality : 0.056 0.726 4053 Planarity : 0.005 0.050 6237 Dihedral : 4.830 58.373 6486 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.40 % Allowed : 7.13 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 1.05 (0.12), residues: 5094 helix: 1.43 (0.20), residues: 627 sheet: 0.99 (0.12), residues: 1782 loop : 0.44 (0.12), residues: 2685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 104 HIS 0.007 0.002 HIS K1051 PHE 0.025 0.003 PHE E 891 TYR 0.025 0.003 TYR E 258 ARG 0.009 0.001 ARG O1100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 210 time to evaluate : 3.337 Fit side-chains REVERT: K 52 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6955 (tm-30) REVERT: K 307 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7743 (tp40) REVERT: K 733 MET cc_start: 0.6993 (OUTLIER) cc_final: 0.6500 (tmm) REVERT: E 307 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: E 653 TYR cc_start: 0.8117 (m-80) cc_final: 0.7912 (m-80) REVERT: E 748 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7286 (mm-40) REVERT: E 998 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7519 (tp40) REVERT: O 307 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: O 733 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6578 (tmm) outliers start: 72 outliers final: 39 residues processed: 251 average time/residue: 1.0871 time to fit residues: 341.3027 Evaluate side-chains 248 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 201 time to evaluate : 3.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 298 SER Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 569 VAL Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 733 MET Chi-restraints excluded: chain K residue 744 ASN Chi-restraints excluded: chain K residue 784 THR Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 969 VAL Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 748 GLN Chi-restraints excluded: chain E residue 784 THR Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 998 GLN Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 298 SER Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 575 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 584 SER Chi-restraints excluded: chain O residue 695 GLU Chi-restraints excluded: chain O residue 712 THR Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 784 THR Chi-restraints excluded: chain O residue 977 LEU Chi-restraints excluded: chain O residue 995 GLN Chi-restraints excluded: chain O residue 998 GLN Chi-restraints excluded: chain O residue 1010 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 472 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 279 optimal weight: 3.9990 chunk 358 optimal weight: 4.9990 chunk 277 optimal weight: 5.9990 chunk 412 optimal weight: 0.6980 chunk 273 optimal weight: 0.0570 chunk 488 optimal weight: 50.0000 chunk 305 optimal weight: 0.0020 chunk 297 optimal weight: 10.0000 chunk 225 optimal weight: 0.3980 overall best weight: 0.3906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 606 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31683 Z= 0.129 Angle : 0.475 11.005 42588 Z= 0.239 Chirality : 0.047 0.699 4053 Planarity : 0.004 0.042 6237 Dihedral : 4.314 57.529 6486 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.03 % Allowed : 9.11 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 1.37 (0.12), residues: 5094 helix: 1.94 (0.20), residues: 639 sheet: 1.18 (0.12), residues: 1776 loop : 0.59 (0.12), residues: 2679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 879 HIS 0.002 0.001 HIS O 207 PHE 0.014 0.001 PHE K1114 TYR 0.028 0.001 TYR K 170 ARG 0.004 0.000 ARG O 570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 210 time to evaluate : 3.547 Fit side-chains REVERT: K 307 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7876 (tp40) REVERT: E 307 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: E 724 MET cc_start: 0.8202 (mtm) cc_final: 0.7931 (mtp) REVERT: E 998 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7373 (tp40) REVERT: O 307 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: O 733 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6414 (tmm) REVERT: O 909 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8462 (tt) outliers start: 43 outliers final: 18 residues processed: 229 average time/residue: 1.0906 time to fit residues: 311.3288 Evaluate side-chains 219 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain E residue 998 GLN Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 298 SER Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 584 SER Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 909 LEU Chi-restraints excluded: chain O residue 998 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 302 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 291 optimal weight: 0.1980 chunk 147 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 310 optimal weight: 0.6980 chunk 332 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 384 optimal weight: 50.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31683 Z= 0.235 Angle : 0.526 13.001 42588 Z= 0.264 Chirality : 0.048 0.469 4053 Planarity : 0.004 0.075 6237 Dihedral : 4.342 53.656 6486 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.27 % Allowed : 9.11 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 1.36 (0.12), residues: 5094 helix: 2.04 (0.21), residues: 624 sheet: 1.22 (0.13), residues: 1743 loop : 0.53 (0.12), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 879 HIS 0.004 0.001 HIS E1051 PHE 0.017 0.002 PHE E 891 TYR 0.022 0.002 TYR K 170 ARG 0.005 0.001 ARG O1100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 211 time to evaluate : 3.431 Fit side-chains REVERT: K 307 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7763 (tp40) REVERT: E 307 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: E 748 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7258 (mm-40) REVERT: E 998 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7446 (tp40) REVERT: O 202 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7588 (mmpt) REVERT: O 307 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: O 733 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6620 (tmm) REVERT: O 909 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8546 (tt) outliers start: 48 outliers final: 30 residues processed: 234 average time/residue: 1.0890 time to fit residues: 319.5593 Evaluate side-chains 242 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 298 SER Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 542 THR Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 608 VAL Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 542 THR Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 748 GLN Chi-restraints excluded: chain E residue 784 THR Chi-restraints excluded: chain E residue 998 GLN Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 202 LYS Chi-restraints excluded: chain O residue 298 SER Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 542 THR Chi-restraints excluded: chain O residue 575 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 584 SER Chi-restraints excluded: chain O residue 695 GLU Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 895 MET Chi-restraints excluded: chain O residue 909 LEU Chi-restraints excluded: chain O residue 977 LEU Chi-restraints excluded: chain O residue 998 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 444 optimal weight: 20.0000 chunk 468 optimal weight: 30.0000 chunk 427 optimal weight: 1.9990 chunk 455 optimal weight: 40.0000 chunk 274 optimal weight: 0.4980 chunk 198 optimal weight: 4.9990 chunk 357 optimal weight: 3.9990 chunk 139 optimal weight: 40.0000 chunk 411 optimal weight: 1.9990 chunk 430 optimal weight: 1.9990 chunk 453 optimal weight: 0.8980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 537 ASN E1128 ASN ** O 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31683 Z= 0.280 Angle : 0.553 11.729 42588 Z= 0.279 Chirality : 0.050 0.547 4053 Planarity : 0.004 0.071 6237 Dihedral : 4.492 53.165 6486 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.41 % Allowed : 9.16 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 1.29 (0.12), residues: 5094 helix: 1.74 (0.20), residues: 645 sheet: 1.25 (0.13), residues: 1734 loop : 0.48 (0.12), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 104 HIS 0.005 0.001 HIS E1051 PHE 0.019 0.002 PHE E 891 TYR 0.022 0.002 TYR E 653 ARG 0.006 0.001 ARG O1100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 211 time to evaluate : 3.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 307 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7742 (tp40) REVERT: K 976 ARG cc_start: 0.7730 (ttm-80) cc_final: 0.7411 (mtm-85) REVERT: E 52 GLN cc_start: 0.7266 (tm-30) cc_final: 0.6879 (tm-30) REVERT: E 307 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: E 748 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7186 (mm-40) REVERT: E 998 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7474 (tp40) REVERT: O 202 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7583 (mmpt) REVERT: O 307 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: O 733 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6606 (tmm) outliers start: 51 outliers final: 30 residues processed: 236 average time/residue: 1.1517 time to fit residues: 341.1173 Evaluate side-chains 237 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 200 time to evaluate : 3.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 298 SER Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 542 THR Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 537 ASN Chi-restraints excluded: chain E residue 542 THR Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 748 GLN Chi-restraints excluded: chain E residue 784 THR Chi-restraints excluded: chain E residue 998 GLN Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 202 LYS Chi-restraints excluded: chain O residue 298 SER Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 542 THR Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 584 SER Chi-restraints excluded: chain O residue 695 GLU Chi-restraints excluded: chain O residue 712 THR Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 977 LEU Chi-restraints excluded: chain O residue 998 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 299 optimal weight: 6.9990 chunk 481 optimal weight: 50.0000 chunk 293 optimal weight: 0.0170 chunk 228 optimal weight: 0.0970 chunk 334 optimal weight: 8.9990 chunk 505 optimal weight: 50.0000 chunk 464 optimal weight: 50.0000 chunk 402 optimal weight: 0.9990 chunk 41 optimal weight: 40.0000 chunk 310 optimal weight: 30.0000 chunk 246 optimal weight: 0.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 537 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 31683 Z= 0.334 Angle : 0.583 12.040 42588 Z= 0.296 Chirality : 0.051 0.538 4053 Planarity : 0.005 0.081 6237 Dihedral : 4.572 53.000 6486 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.94 % Allowed : 9.87 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.18 (0.12), residues: 5094 helix: 1.58 (0.20), residues: 645 sheet: 1.27 (0.13), residues: 1707 loop : 0.37 (0.12), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP O 104 HIS 0.005 0.001 HIS K1051 PHE 0.024 0.002 PHE E 536 TYR 0.023 0.002 TYR E 653 ARG 0.008 0.001 ARG O 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 198 time to evaluate : 3.296 Fit side-chains revert: symmetry clash REVERT: K 307 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7762 (tp40) REVERT: E 52 GLN cc_start: 0.7288 (tm-30) cc_final: 0.6893 (tm-30) REVERT: E 229 LEU cc_start: 0.6438 (mt) cc_final: 0.6128 (mt) REVERT: E 307 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: E 998 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7502 (tp40) REVERT: O 307 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: O 733 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6629 (tmm) outliers start: 41 outliers final: 29 residues processed: 221 average time/residue: 1.0365 time to fit residues: 288.2719 Evaluate side-chains 230 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 298 SER Chi-restraints excluded: chain K residue 307 GLN Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 581 THR Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 712 THR Chi-restraints excluded: chain K residue 871 LEU Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 995 GLN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 784 THR Chi-restraints excluded: chain E residue 998 GLN Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 298 SER Chi-restraints excluded: chain O residue 307 GLN Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain O residue 584 SER Chi-restraints excluded: chain O residue 695 GLU Chi-restraints excluded: chain O residue 712 THR Chi-restraints excluded: chain O residue 733 MET Chi-restraints excluded: chain O residue 784 THR Chi-restraints excluded: chain O residue 977 LEU Chi-restraints excluded: chain O residue 998 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 319 optimal weight: 50.0000 chunk 428 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 370 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 111 optimal weight: 40.0000 chunk 402 optimal weight: 0.7980 chunk 168 optimal weight: 0.1980 chunk 413 optimal weight: 1.9990 chunk 51 optimal weight: 0.0020 chunk 74 optimal weight: 2.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.240490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.205582 restraints weight = 37354.831| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 1.96 r_work: 0.4033 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31683 Z= 0.164 Angle : 0.492 11.091 42588 Z= 0.247 Chirality : 0.047 0.499 4053 Planarity : 0.004 0.083 6237 Dihedral : 4.311 53.885 6486 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.84 % Allowed : 9.92 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 1.40 (0.12), residues: 5094 helix: 2.01 (0.20), residues: 642 sheet: 1.36 (0.13), residues: 1716 loop : 0.47 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 879 HIS 0.002 0.001 HIS E1057 PHE 0.016 0.001 PHE K1114 TYR 0.021 0.001 TYR K 170 ARG 0.007 0.001 ARG O 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9228.72 seconds wall clock time: 166 minutes 44.41 seconds (10004.41 seconds total)