Starting phenix.real_space_refine on Tue Feb 20 03:35:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv6_22494/02_2024/7jv6_22494.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv6_22494/02_2024/7jv6_22494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv6_22494/02_2024/7jv6_22494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv6_22494/02_2024/7jv6_22494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv6_22494/02_2024/7jv6_22494.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv6_22494/02_2024/7jv6_22494.pdb" } resolution = 3.0 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= 0.076 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 114 5.16 5 C 16832 2.51 5 N 4476 2.21 5 O 5226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 309": "OE1" <-> "OE2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 428": "OD1" <-> "OD2" Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 663": "OD1" <-> "OD2" Residue "E PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1072": "OE1" <-> "OE2" Residue "E PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26648 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7476 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 48, 'TRANS': 928} Chain breaks: 11 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 107 Chain: "H" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 582 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 9, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 215 Chain: "L" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 544 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 149 Chain: "B" Number of atoms: 7476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7476 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 48, 'TRANS': 928} Chain breaks: 11 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 107 Chain: "C" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 582 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 9, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 215 Chain: "D" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 544 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 149 Chain: "E" Number of atoms: 7476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7476 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 48, 'TRANS': 928} Chain breaks: 11 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 107 Chain: "F" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 582 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 9, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 215 Chain: "G" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 546 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 149 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 13.64, per 1000 atoms: 0.51 Number of scatterers: 26648 At special positions: 0 Unit cell: (137.55, 145.95, 191.1, 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 114 16.00 O 5226 8.00 N 4476 7.00 C 16832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.33 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.01 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.33 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.01 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.02 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.06 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.33 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.02 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.02 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.01 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 BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B 165 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 122 " " NAG E1303 " - " ASN E 234 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 343 " " NAG E1307 " - " ASN E 603 " " NAG E1308 " - " ASN E 616 " " NAG E1309 " - " ASN E 657 " " NAG E1310 " - " ASN E 709 " " NAG E1311 " - " ASN E1074 " " NAG E1312 " - " ASN E 165 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN E 717 " " NAG S 1 " - " ASN E 801 " " NAG T 1 " - " ASN E1098 " " NAG U 1 " - " ASN E1134 " Time building additional restraints: 11.38 Conformation dependent library (CDL) restraints added in 5.6 seconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6690 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 66 sheets defined 21.8% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.194A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 501 through 501 No H-bonds generated for 'chain 'A' and resid 501 through 501' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.827A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.561A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.879A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.008A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'L' and resid 30 through 34 Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.195A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 501 through 501 No H-bonds generated for 'chain 'B' and resid 501 through 501' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.827A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.561A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.879A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.008A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.194A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 501 through 501 No H-bonds generated for 'chain 'E' and resid 501 through 501' Processing helix chain 'E' and resid 503 through 505 No H-bonds generated for 'chain 'E' and resid 503 through 505' Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.827A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 891 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 913 through 919 Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.561A pdb=" N SER E 940 " --> pdb=" O ASP E 936 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.879A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 982 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 5.008A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'G' and resid 30 through 34 Processing helix chain 'G' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.007A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.822A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.308A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.596A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.721A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.283A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.863A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE A 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.119A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.119A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.444A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.917A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.671A pdb=" N ALA A 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.394A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.394A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.722A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.851A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.635A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AC7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.006A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.822A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.308A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.596A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.722A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.283A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.119A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.119A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.444A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.917A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.394A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.394A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE3, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.722A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'C' and resid 11 through 12 removed outlier: 5.850A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AE8, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AE9, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.635A pdb=" N TRP D 37 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AF2, first strand: chain 'E' and resid 28 through 30 removed outlier: 8.007A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N HIS E 207 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 9.788A pdb=" N LEU E 223 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 47 through 55 removed outlier: 7.308A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.596A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.721A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.282A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.119A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.119A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.444A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AG2, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.917A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.394A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN E 717 " --> pdb=" O ALA E1070 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.394A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN E 717 " --> pdb=" O ALA E1070 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AG6, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.722A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'F' and resid 11 through 12 removed outlier: 5.850A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AH1, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AH2, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.635A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 9 through 12 1284 hydrogen bonds defined for protein. 3447 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: 14.85 Time building geometry restraints manager: 12.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 8292 1.34 - 1.48: 7818 1.48 - 1.63: 10911 1.63 - 1.78: 24 1.78 - 1.92: 114 Bond restraints: 27159 Sorted by residual: bond pdb=" CB LEU A1145 " pdb=" CG LEU A1145 " ideal model delta sigma weight residual 1.530 1.604 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" CB LEU E1145 " pdb=" CG LEU E1145 " ideal model delta sigma weight residual 1.530 1.604 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CB LEU B1145 " pdb=" CG LEU B1145 " ideal model delta sigma weight residual 1.530 1.604 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CB ASN B 422 " pdb=" CG ASN B 422 " ideal model delta sigma weight residual 1.516 1.425 0.091 2.50e-02 1.60e+03 1.33e+01 bond pdb=" CB ASN E 422 " pdb=" CG ASN E 422 " ideal model delta sigma weight residual 1.516 1.425 0.091 2.50e-02 1.60e+03 1.32e+01 ... (remaining 27154 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.44: 813 106.44 - 113.32: 14592 113.32 - 120.20: 9816 120.20 - 127.08: 11780 127.08 - 133.95: 90 Bond angle restraints: 37091 Sorted by residual: angle pdb=" C ASP E1139 " pdb=" N PRO E1140 " pdb=" CA PRO E1140 " ideal model delta sigma weight residual 119.56 127.01 -7.45 1.02e+00 9.61e-01 5.33e+01 angle pdb=" C ASP B1139 " pdb=" N PRO B1140 " pdb=" CA PRO B1140 " ideal model delta sigma weight residual 119.56 126.99 -7.43 1.02e+00 9.61e-01 5.30e+01 angle pdb=" C ASP A1139 " pdb=" N PRO A1140 " pdb=" CA PRO A1140 " ideal model delta sigma weight residual 119.56 126.98 -7.42 1.02e+00 9.61e-01 5.29e+01 angle pdb=" C LYS E 811 " pdb=" N PRO E 812 " pdb=" CA PRO E 812 " ideal model delta sigma weight residual 119.56 126.60 -7.04 1.02e+00 9.61e-01 4.77e+01 angle pdb=" C LYS B 811 " pdb=" N PRO B 812 " pdb=" CA PRO B 812 " ideal model delta sigma weight residual 119.56 126.60 -7.04 1.02e+00 9.61e-01 4.77e+01 ... (remaining 37086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 16209 17.64 - 35.29: 486 35.29 - 52.93: 72 52.93 - 70.58: 57 70.58 - 88.22: 18 Dihedral angle restraints: 16842 sinusoidal: 6459 harmonic: 10383 Sorted by residual: dihedral pdb=" CB CYS E1032 " pdb=" SG CYS E1032 " pdb=" SG CYS E1043 " pdb=" CB CYS E1043 " ideal model delta sinusoidal sigma weight residual 93.00 170.84 -77.84 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 170.83 -77.83 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 170.83 -77.83 1 1.00e+01 1.00e-02 7.58e+01 ... (remaining 16839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3470 0.093 - 0.186: 758 0.186 - 0.278: 191 0.278 - 0.371: 66 0.371 - 0.464: 27 Chirality restraints: 4512 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.55e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.39e+01 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.28e+01 ... (remaining 4509 not shown) Planarity restraints: 4858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 331 " -0.051 2.00e-02 2.50e+03 5.12e-02 3.28e+01 pdb=" CG ASN E 331 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN E 331 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN E 331 " 0.077 2.00e-02 2.50e+03 pdb=" C1 NAG E1305 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.050 2.00e-02 2.50e+03 5.09e-02 3.24e+01 pdb=" CG ASN B 331 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.076 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.050 2.00e-02 2.50e+03 5.07e-02 3.21e+01 pdb=" CG ASN A 331 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.076 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.061 2.00e-02 2.50e+03 ... (remaining 4855 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 10827 2.90 - 3.40: 24007 3.40 - 3.90: 44277 3.90 - 4.40: 49947 4.40 - 4.90: 82746 Nonbonded interactions: 211804 Sorted by model distance: nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.402 2.520 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.402 2.520 nonbonded pdb=" NZ LYS E1028 " pdb=" O PHE E1042 " model vdw 2.402 2.520 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.409 2.520 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.409 2.520 ... (remaining 211799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'D' and (resid 2 through 81 or (resid 82 through 89 and (name N or name C \ A or name C or name O or name CB )) or resid 90 through 110)) selection = (chain 'G' and (resid 2 through 34 or (resid 35 through 41 and (name N or name C \ A or name C or name O or name CB )) or resid 42 through 81 or (resid 82 through \ 89 and (name N or name CA or name C or name O or name CB )) or resid 90 through \ 110)) selection = (chain 'L' and (resid 2 through 34 or (resid 35 through 41 and (name N or name C \ A or name C or name O or name CB )) or resid 42 through 110)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.450 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 78.230 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.340 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:14.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 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 : 0.014 0.115 27159 Z= 0.962 Angle : 1.405 7.613 37091 Z= 0.951 Chirality : 0.095 0.464 4512 Planarity : 0.005 0.026 4810 Dihedral : 9.824 88.223 10017 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.13), residues: 3528 helix: 0.02 (0.18), residues: 705 sheet: 0.69 (0.16), residues: 942 loop : 0.64 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.005 TRP A 886 HIS 0.005 0.001 HIS B1048 PHE 0.022 0.003 PHE E 515 TYR 0.036 0.004 TYR E 495 ARG 0.002 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 545 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6255 (p0) cc_final: 0.5903 (m-40) REVERT: A 561 PRO cc_start: 0.5802 (Cg_exo) cc_final: 0.5564 (Cg_endo) REVERT: B 81 ASN cc_start: 0.6247 (p0) cc_final: 0.5919 (m-40) REVERT: B 1050 MET cc_start: 0.8419 (ptt) cc_final: 0.8188 (ptm) REVERT: E 32 PHE cc_start: 0.6124 (m-80) cc_final: 0.5914 (m-80) REVERT: E 81 ASN cc_start: 0.6177 (p0) cc_final: 0.5785 (m-40) REVERT: E 960 ASN cc_start: 0.7718 (m-40) cc_final: 0.7464 (m-40) outliers start: 0 outliers final: 1 residues processed: 545 average time/residue: 1.0725 time to fit residues: 703.3034 Evaluate side-chains 255 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 770 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 0.8980 chunk 268 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 277 optimal weight: 0.7980 chunk 107 optimal weight: 0.0170 chunk 168 optimal weight: 0.7980 chunk 206 optimal weight: 0.5980 chunk 321 optimal weight: 0.7980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 762 GLN A 764 ASN A 804 GLN A 907 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 764 ASN B 784 GLN B 935 GLN B 957 GLN B1135 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 ASN E 784 GLN ** E 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 957 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27159 Z= 0.240 Angle : 0.610 10.204 37091 Z= 0.330 Chirality : 0.046 0.195 4512 Planarity : 0.004 0.031 4810 Dihedral : 5.068 28.855 5045 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.41 % Allowed : 8.33 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 3528 helix: 1.32 (0.20), residues: 675 sheet: 0.30 (0.15), residues: 1008 loop : 0.33 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.004 0.001 HIS B1083 PHE 0.018 0.002 PHE B 140 TYR 0.022 0.002 TYR E 495 ARG 0.006 0.001 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 279 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 875 SER cc_start: 0.8430 (t) cc_final: 0.8105 (m) REVERT: B 868 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: B 1125 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.8040 (p0) REVERT: E 81 ASN cc_start: 0.6210 (p0) cc_final: 0.6006 (m-40) REVERT: E 960 ASN cc_start: 0.7617 (m-40) cc_final: 0.7381 (m-40) outliers start: 84 outliers final: 38 residues processed: 333 average time/residue: 1.0188 time to fit residues: 414.5655 Evaluate side-chains 237 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain E residue 658 ASN Chi-restraints excluded: chain E residue 702 GLU Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain E residue 1084 ASP Chi-restraints excluded: chain E residue 1123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 267 optimal weight: 7.9990 chunk 218 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 322 optimal weight: 1.9990 chunk 347 optimal weight: 7.9990 chunk 286 optimal weight: 0.9980 chunk 319 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 258 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 239 GLN B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 957 GLN E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN E 935 GLN E 957 GLN E1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 27159 Z= 0.357 Angle : 0.606 9.079 37091 Z= 0.325 Chirality : 0.047 0.220 4512 Planarity : 0.004 0.053 4810 Dihedral : 4.777 29.758 5043 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.35 % Allowed : 10.20 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.13), residues: 3528 helix: 1.34 (0.20), residues: 675 sheet: -0.07 (0.15), residues: 981 loop : -0.04 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 886 HIS 0.006 0.002 HIS B1083 PHE 0.019 0.002 PHE E 58 TYR 0.021 0.002 TYR E 365 ARG 0.005 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 212 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7228 (ttt90) cc_final: 0.7024 (ttt90) REVERT: A 418 ILE cc_start: 0.8202 (mp) cc_final: 0.7844 (mt) REVERT: A 1092 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7284 (mt-10) REVERT: A 1139 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.6427 (p0) REVERT: B 868 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: B 1139 ASP cc_start: 0.6909 (OUTLIER) cc_final: 0.6567 (p0) REVERT: E 81 ASN cc_start: 0.6435 (p0) cc_final: 0.5931 (m-40) REVERT: E 960 ASN cc_start: 0.7828 (m-40) cc_final: 0.7588 (m-40) REVERT: E 1086 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8009 (mtpt) REVERT: E 1139 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6700 (p0) outliers start: 107 outliers final: 48 residues processed: 297 average time/residue: 1.0636 time to fit residues: 384.0751 Evaluate side-chains 230 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 177 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 658 ASN Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1086 LYS Chi-restraints excluded: chain E residue 1139 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 216 optimal weight: 20.0000 chunk 323 optimal weight: 1.9990 chunk 342 optimal weight: 50.0000 chunk 168 optimal weight: 0.9990 chunk 306 optimal weight: 0.9990 chunk 92 optimal weight: 0.2980 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 957 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 764 ASN E 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 27159 Z= 0.321 Angle : 0.579 10.242 37091 Z= 0.307 Chirality : 0.046 0.247 4512 Planarity : 0.004 0.041 4810 Dihedral : 4.767 33.262 5043 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.98 % Allowed : 11.21 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3528 helix: 1.19 (0.20), residues: 681 sheet: -0.37 (0.14), residues: 1035 loop : -0.20 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 886 HIS 0.006 0.001 HIS A 245 PHE 0.024 0.002 PHE A 140 TYR 0.018 0.002 TYR E 269 ARG 0.006 0.001 ARG E 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 193 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6626 (mtp-110) REVERT: A 357 ARG cc_start: 0.7370 (ttt90) cc_final: 0.7105 (ttt90) REVERT: A 418 ILE cc_start: 0.8314 (mp) cc_final: 0.7994 (mt) REVERT: A 1092 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7289 (mt-10) REVERT: A 1139 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6464 (p0) REVERT: B 287 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.7013 (m-30) REVERT: B 1139 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6668 (p0) REVERT: E 81 ASN cc_start: 0.6466 (p0) cc_final: 0.5852 (m-40) REVERT: E 319 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6652 (mtp-110) REVERT: E 592 PHE cc_start: 0.7331 (p90) cc_final: 0.6972 (p90) REVERT: E 960 ASN cc_start: 0.7776 (m-40) cc_final: 0.7564 (m-40) REVERT: E 1086 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8041 (mtpt) REVERT: E 1113 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7241 (mt0) outliers start: 98 outliers final: 57 residues processed: 277 average time/residue: 1.1087 time to fit residues: 369.7745 Evaluate side-chains 230 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 166 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 465 GLU Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 658 ASN Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 957 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1086 LYS Chi-restraints excluded: chain E residue 1113 GLN Chi-restraints excluded: chain E residue 1127 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 254 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 291 optimal weight: 0.6980 chunk 236 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 chunk 307 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1106 GLN E 239 GLN ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27159 Z= 0.242 Angle : 0.534 8.624 37091 Z= 0.283 Chirality : 0.044 0.240 4512 Planarity : 0.004 0.038 4810 Dihedral : 4.610 32.683 5043 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.78 % Allowed : 12.72 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3528 helix: 1.33 (0.20), residues: 678 sheet: -0.17 (0.15), residues: 933 loop : -0.33 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 886 HIS 0.004 0.001 HIS B 207 PHE 0.018 0.002 PHE E 194 TYR 0.019 0.002 TYR E 396 ARG 0.006 0.000 ARG E 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 174 time to evaluate : 3.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6635 (mtp-110) REVERT: A 357 ARG cc_start: 0.7196 (ttt90) cc_final: 0.6953 (ttt90) REVERT: A 869 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8442 (mtt) REVERT: A 1139 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6529 (p0) REVERT: B 287 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7002 (m-30) REVERT: B 1139 ASP cc_start: 0.7010 (OUTLIER) cc_final: 0.6642 (p0) REVERT: E 81 ASN cc_start: 0.6405 (p0) cc_final: 0.5755 (m-40) REVERT: E 319 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6643 (mtp-110) REVERT: E 418 ILE cc_start: 0.8167 (mp) cc_final: 0.7862 (mt) outliers start: 93 outliers final: 55 residues processed: 252 average time/residue: 1.0799 time to fit residues: 329.4992 Evaluate side-chains 227 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 166 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 50.0000 chunk 308 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 200 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 342 optimal weight: 20.0000 chunk 284 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 607 GLN A 957 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 957 GLN E1106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 27159 Z= 0.369 Angle : 0.590 8.381 37091 Z= 0.311 Chirality : 0.047 0.268 4512 Planarity : 0.004 0.038 4810 Dihedral : 4.992 40.576 5043 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.27 % Allowed : 12.80 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3528 helix: 1.19 (0.20), residues: 675 sheet: -0.23 (0.15), residues: 906 loop : -0.42 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 886 HIS 0.004 0.002 HIS B 245 PHE 0.022 0.002 PHE A 140 TYR 0.019 0.002 TYR E 200 ARG 0.007 0.001 ARG E 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 187 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6679 (mtp-110) REVERT: A 357 ARG cc_start: 0.7242 (ttt90) cc_final: 0.6992 (ttt90) REVERT: A 392 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.6824 (m-80) REVERT: A 418 ILE cc_start: 0.8241 (mp) cc_final: 0.8003 (mt) REVERT: A 1139 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6619 (p0) REVERT: A 1142 GLN cc_start: 0.7129 (tp40) cc_final: 0.6850 (tp40) REVERT: B 287 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7057 (m-30) REVERT: B 569 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7608 (mt) REVERT: B 1139 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6749 (p0) REVERT: E 81 ASN cc_start: 0.6506 (p0) cc_final: 0.5782 (m-40) REVERT: E 319 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6708 (mtp-110) REVERT: E 418 ILE cc_start: 0.8202 (mp) cc_final: 0.7925 (mt) REVERT: E 1086 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8047 (mtpt) outliers start: 105 outliers final: 69 residues processed: 277 average time/residue: 1.0370 time to fit residues: 348.9735 Evaluate side-chains 250 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 173 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1086 LYS Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1127 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 195 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 288 optimal weight: 0.9980 chunk 191 optimal weight: 0.5980 chunk 341 optimal weight: 40.0000 chunk 213 optimal weight: 1.9990 chunk 208 optimal weight: 0.4980 chunk 157 optimal weight: 0.0040 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 957 GLN E 239 GLN ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27159 Z= 0.184 Angle : 0.504 7.669 37091 Z= 0.266 Chirality : 0.044 0.218 4512 Planarity : 0.003 0.037 4810 Dihedral : 4.557 39.486 5043 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.29 % Allowed : 14.34 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3528 helix: 1.52 (0.21), residues: 678 sheet: -0.21 (0.16), residues: 882 loop : -0.42 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.005 0.001 HIS B 207 PHE 0.022 0.001 PHE A 140 TYR 0.018 0.001 TYR A 453 ARG 0.006 0.000 ARG E 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 195 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6588 (mtp-110) REVERT: A 357 ARG cc_start: 0.7186 (ttt90) cc_final: 0.6960 (ttt90) REVERT: A 392 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.6843 (m-80) REVERT: A 418 ILE cc_start: 0.8235 (mp) cc_final: 0.7953 (mt) REVERT: A 869 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8520 (mtt) REVERT: A 1139 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6679 (p0) REVERT: A 1142 GLN cc_start: 0.7052 (tp40) cc_final: 0.6771 (tp40) REVERT: B 569 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7506 (mt) REVERT: B 868 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: B 1139 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6733 (p0) REVERT: E 81 ASN cc_start: 0.6145 (p0) cc_final: 0.5417 (m-40) REVERT: E 319 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6638 (mtp-110) REVERT: E 418 ILE cc_start: 0.8138 (mp) cc_final: 0.7882 (mt) REVERT: E 567 ARG cc_start: 0.7233 (mmm-85) cc_final: 0.7013 (mmm-85) REVERT: E 592 PHE cc_start: 0.7276 (p90) cc_final: 0.7040 (p90) REVERT: E 1086 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8052 (mtpt) outliers start: 81 outliers final: 42 residues processed: 265 average time/residue: 1.1062 time to fit residues: 354.7591 Evaluate side-chains 232 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 181 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1086 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 203 optimal weight: 0.5980 chunk 102 optimal weight: 40.0000 chunk 67 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 216 optimal weight: 8.9990 chunk 232 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 31 optimal weight: 0.0020 chunk 268 optimal weight: 4.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 965 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27159 Z= 0.203 Angle : 0.506 7.468 37091 Z= 0.266 Chirality : 0.044 0.221 4512 Planarity : 0.003 0.039 4810 Dihedral : 4.477 38.950 5043 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.93 % Allowed : 15.20 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3528 helix: 1.60 (0.21), residues: 675 sheet: -0.20 (0.16), residues: 882 loop : -0.42 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 886 HIS 0.004 0.001 HIS B 207 PHE 0.024 0.001 PHE E 194 TYR 0.018 0.001 TYR A 453 ARG 0.004 0.000 ARG E 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 186 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6686 (mtp-110) REVERT: A 357 ARG cc_start: 0.7180 (ttt90) cc_final: 0.6853 (tmt-80) REVERT: A 392 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.6831 (m-80) REVERT: A 418 ILE cc_start: 0.8175 (mp) cc_final: 0.7925 (mt) REVERT: A 869 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8516 (mtt) REVERT: A 1139 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6697 (p0) REVERT: A 1142 GLN cc_start: 0.7155 (tp40) cc_final: 0.6822 (tp40) REVERT: B 868 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: B 1139 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6740 (p0) REVERT: E 81 ASN cc_start: 0.6229 (p0) cc_final: 0.5415 (m-40) REVERT: E 319 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6672 (mtp-110) REVERT: E 418 ILE cc_start: 0.8161 (mp) cc_final: 0.7903 (mt) REVERT: E 592 PHE cc_start: 0.7303 (p90) cc_final: 0.7053 (p90) REVERT: E 1086 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8023 (mtpt) outliers start: 72 outliers final: 47 residues processed: 250 average time/residue: 1.0978 time to fit residues: 330.5821 Evaluate side-chains 230 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 175 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1086 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 1.9990 chunk 326 optimal weight: 0.7980 chunk 298 optimal weight: 1.9990 chunk 317 optimal weight: 0.7980 chunk 191 optimal weight: 0.1980 chunk 138 optimal weight: 0.9990 chunk 249 optimal weight: 0.8980 chunk 97 optimal weight: 50.0000 chunk 287 optimal weight: 0.0870 chunk 300 optimal weight: 2.9990 chunk 316 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1106 GLN B1142 GLN E 239 GLN ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27159 Z= 0.179 Angle : 0.494 7.634 37091 Z= 0.261 Chirality : 0.044 0.212 4512 Planarity : 0.003 0.040 4810 Dihedral : 4.351 37.745 5043 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.13 % Allowed : 15.48 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3528 helix: 1.66 (0.21), residues: 672 sheet: -0.17 (0.16), residues: 882 loop : -0.39 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 436 HIS 0.004 0.001 HIS B 207 PHE 0.025 0.001 PHE E 194 TYR 0.017 0.001 TYR A 453 ARG 0.005 0.000 ARG E 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 180 time to evaluate : 2.772 Fit side-chains revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6594 (mtp-110) REVERT: A 357 ARG cc_start: 0.7209 (ttt90) cc_final: 0.6851 (tmt-80) REVERT: A 392 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.6744 (m-80) REVERT: A 418 ILE cc_start: 0.8134 (mp) cc_final: 0.7894 (mt) REVERT: A 869 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8514 (mtt) REVERT: A 1139 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6685 (p0) REVERT: A 1142 GLN cc_start: 0.7170 (tp40) cc_final: 0.6839 (tp40) REVERT: B 868 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: B 1139 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6777 (p0) REVERT: E 81 ASN cc_start: 0.6340 (p0) cc_final: 0.5523 (m-40) REVERT: E 319 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6752 (mtp-110) REVERT: E 418 ILE cc_start: 0.8169 (mp) cc_final: 0.7926 (mt) REVERT: E 592 PHE cc_start: 0.7328 (p90) cc_final: 0.7065 (p90) outliers start: 77 outliers final: 51 residues processed: 247 average time/residue: 1.1019 time to fit residues: 331.1929 Evaluate side-chains 227 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 169 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 0.8980 chunk 336 optimal weight: 50.0000 chunk 205 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 233 optimal weight: 50.0000 chunk 352 optimal weight: 1.9990 chunk 324 optimal weight: 0.7980 chunk 280 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 216 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN B1142 GLN E 239 GLN ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 965 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 27159 Z= 0.299 Angle : 0.546 7.579 37091 Z= 0.287 Chirality : 0.046 0.349 4512 Planarity : 0.004 0.045 4810 Dihedral : 4.668 42.607 5043 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.84 % Allowed : 15.81 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3528 helix: 1.67 (0.21), residues: 651 sheet: -0.29 (0.16), residues: 888 loop : -0.50 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.004 0.001 HIS A 207 PHE 0.025 0.002 PHE E 194 TYR 0.018 0.002 TYR A 453 ARG 0.003 0.000 ARG B 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 173 time to evaluate : 3.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6653 (mtp-110) REVERT: A 392 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.6716 (m-80) REVERT: A 418 ILE cc_start: 0.8173 (mp) cc_final: 0.7930 (mt) REVERT: A 1092 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: A 1139 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6716 (p0) REVERT: A 1142 GLN cc_start: 0.7212 (tp40) cc_final: 0.6869 (tp40) REVERT: B 201 PHE cc_start: 0.7383 (t80) cc_final: 0.6982 (t80) REVERT: B 237 ARG cc_start: 0.6103 (OUTLIER) cc_final: 0.5702 (ptt-90) REVERT: B 1139 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6810 (p0) REVERT: E 81 ASN cc_start: 0.6503 (p0) cc_final: 0.5577 (m-40) REVERT: E 319 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6678 (mtp-110) REVERT: E 418 ILE cc_start: 0.8183 (mp) cc_final: 0.7950 (mt) REVERT: E 592 PHE cc_start: 0.7363 (p90) cc_final: 0.7076 (p90) outliers start: 70 outliers final: 44 residues processed: 234 average time/residue: 1.0854 time to fit residues: 307.5307 Evaluate side-chains 219 residues out of total 3102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 168 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 40.0000 chunk 299 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 258 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 281 optimal weight: 0.7980 chunk 117 optimal weight: 30.0000 chunk 288 optimal weight: 0.7980 chunk 35 optimal weight: 0.0270 chunk 51 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN E 239 GLN E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 965 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.190161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.158049 restraints weight = 34343.498| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.52 r_work: 0.3717 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 27159 Z= 0.204 Angle : 0.510 7.453 37091 Z= 0.269 Chirality : 0.044 0.279 4512 Planarity : 0.003 0.044 4810 Dihedral : 4.516 42.862 5043 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.44 % Allowed : 16.29 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3528 helix: 1.59 (0.21), residues: 672 sheet: -0.29 (0.16), residues: 891 loop : -0.46 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 886 HIS 0.004 0.001 HIS B 207 PHE 0.026 0.001 PHE E 194 TYR 0.017 0.001 TYR A 453 ARG 0.003 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7473.95 seconds wall clock time: 134 minutes 33.70 seconds (8073.70 seconds total)