Starting phenix.real_space_refine on Sun Mar 24 06:27:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqo_11871/03_2024/7aqo_11871.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqo_11871/03_2024/7aqo_11871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqo_11871/03_2024/7aqo_11871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqo_11871/03_2024/7aqo_11871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqo_11871/03_2024/7aqo_11871.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqo_11871/03_2024/7aqo_11871.pdb" } resolution = 4.5 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= 0.060 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 136 5.16 5 C 25983 2.51 5 N 6865 2.21 5 O 7277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 59": "OD1" <-> "OD2" Residue "G PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 225": "OD1" <-> "OD2" Residue "G GLU 268": "OE1" <-> "OE2" Residue "G TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 322": "OE1" <-> "OE2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "G ARG 439": "NH1" <-> "NH2" Residue "G TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 610": "NH1" <-> "NH2" Residue "G GLU 636": "OE1" <-> "OE2" Residue "G ARG 637": "NH1" <-> "NH2" Residue "G GLU 638": "OE1" <-> "OE2" Residue "G ARG 656": "NH1" <-> "NH2" Residue "G ARG 709": "NH1" <-> "NH2" Residue "G ARG 714": "NH1" <-> "NH2" Residue "G ARG 820": "NH1" <-> "NH2" Residue "G TYR 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 860": "OD1" <-> "OD2" Residue "G GLU 861": "OE1" <-> "OE2" Residue "G TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1041": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 27": "OD1" <-> "OD2" Residue "H ARG 30": "NH1" <-> "NH2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 122": "OE1" <-> "OE2" Residue "H PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 176": "OE1" <-> "OE2" Residue "H PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 224": "NH1" <-> "NH2" Residue "H PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 313": "NH1" <-> "NH2" Residue "H TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 410": "NH1" <-> "NH2" Residue "H PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 429": "OE1" <-> "OE2" Residue "H ARG 459": "NH1" <-> "NH2" Residue "H PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 476": "NH1" <-> "NH2" Residue "H PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 584": "NH1" <-> "NH2" Residue "K TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "K ARG 82": "NH1" <-> "NH2" Residue "K PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 153": "NH1" <-> "NH2" Residue "K TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 266": "NH1" <-> "NH2" Residue "K PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 323": "OD1" <-> "OD2" Residue "L GLU 72": "OE1" <-> "OE2" Residue "L ASP 79": "OD1" <-> "OD2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L ASP 101": "OD1" <-> "OD2" Residue "L PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 174": "OD1" <-> "OD2" Residue "L ASP 182": "OD1" <-> "OD2" Residue "L TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 205": "OD1" <-> "OD2" Residue "L GLU 223": "OE1" <-> "OE2" Residue "L ASP 225": "OD1" <-> "OD2" Residue "L ARG 228": "NH1" <-> "NH2" Residue "L ASP 229": "OD1" <-> "OD2" Residue "L PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 292": "OE1" <-> "OE2" Residue "L ASP 302": "OD1" <-> "OD2" Residue "L ASP 303": "OD1" <-> "OD2" Residue "L GLU 343": "OE1" <-> "OE2" Residue "L GLU 344": "OE1" <-> "OE2" Residue "L PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 414": "OE1" <-> "OE2" Residue "L GLU 424": "OE1" <-> "OE2" Residue "L PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 427": "OD1" <-> "OD2" Residue "L ASP 439": "OD1" <-> "OD2" Residue "L TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A ARG 637": "NH1" <-> "NH2" Residue "A GLU 638": "OE1" <-> "OE2" Residue "A ARG 656": "NH1" <-> "NH2" Residue "A ARG 709": "NH1" <-> "NH2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A TYR 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 860": "OD1" <-> "OD2" Residue "A GLU 861": "OE1" <-> "OE2" Residue "A TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1041": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 266": "NH1" <-> "NH2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 323": "OD1" <-> "OD2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F ASP 79": "OD1" <-> "OD2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F ASP 101": "OD1" <-> "OD2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 174": "OD1" <-> "OD2" Residue "F ASP 182": "OD1" <-> "OD2" Residue "F TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 205": "OD1" <-> "OD2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "F ASP 225": "OD1" <-> "OD2" Residue "F ARG 228": "NH1" <-> "NH2" Residue "F ASP 229": "OD1" <-> "OD2" Residue "F PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 292": "OE1" <-> "OE2" Residue "F ASP 302": "OD1" <-> "OD2" Residue "F ASP 303": "OD1" <-> "OD2" Residue "F GLU 343": "OE1" <-> "OE2" Residue "F GLU 344": "OE1" <-> "OE2" Residue "F PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 414": "OE1" <-> "OE2" Residue "F GLU 424": "OE1" <-> "OE2" Residue "F PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 427": "OD1" <-> "OD2" Residue "F ASP 439": "OD1" <-> "OD2" Residue "F TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 88": "NH1" <-> "NH2" Residue "J ARG 116": "NH1" <-> "NH2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I GLU 90": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 95": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40261 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 7785 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 297} Link IDs: {'PTRANS': 31, 'TRANS': 1047} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1009 Unresolved non-hydrogen angles: 1256 Unresolved non-hydrogen dihedrals: 806 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 28, 'TRP:plan': 2, 'ASP:plan': 33, 'PHE:plan': 6, 'GLU:plan': 50, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 609 Chain: "H" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4143 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 22, 'TRANS': 540} Chain breaks: 3 Unresolved non-hydrogen bonds: 560 Unresolved non-hydrogen angles: 680 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 15, 'ASP:plan': 24, 'PHE:plan': 2, 'GLU:plan': 35, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 358 Chain: "K" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2357 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 8, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 447 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 19, 'TYR:plan': 1, 'ASN:plan1': 12, 'HIS:plan': 2, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 171 Chain: "L" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2818 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 14, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 7785 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 297} Link IDs: {'PTRANS': 31, 'TRANS': 1047} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1009 Unresolved non-hydrogen angles: 1256 Unresolved non-hydrogen dihedrals: 806 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 28, 'TRP:plan': 2, 'ASP:plan': 33, 'PHE:plan': 6, 'GLU:plan': 50, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 609 Chain: "B" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4143 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 22, 'TRANS': 540} Chain breaks: 3 Unresolved non-hydrogen bonds: 560 Unresolved non-hydrogen angles: 680 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 15, 'ASP:plan': 24, 'PHE:plan': 2, 'GLU:plan': 35, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 358 Chain: "E" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2357 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 8, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 447 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 19, 'TYR:plan': 1, 'ASN:plan1': 12, 'HIS:plan': 2, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 171 Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2818 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 14, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "J" Number of atoms: 1588 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 230, 1583 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 14, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 167 Conformer: "B" Number of residues, atoms: 230, 1583 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 14, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 167 bond proxies already assigned to first conformer: 1598 Chain: "I" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1452 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 391 Unresolved non-hydrogen angles: 488 Unresolved non-hydrogen dihedrals: 322 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 213 Chain: "C" Number of atoms: 1573 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1568 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 13, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 164 Conformer: "B" Number of residues, atoms: 227, 1568 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 13, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 164 bond proxies already assigned to first conformer: 1584 Chain: "D" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1442 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 382 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 205 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALEU J 47 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLEU J 47 " occ=0.50 residue: pdb=" N ALEU C 47 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLEU C 47 " occ=0.50 Time building chain proxies: 22.71, per 1000 atoms: 0.56 Number of scatterers: 40261 At special positions: 0 Unit cell: (157.32, 222.18, 314.64, 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 136 16.00 O 7277 8.00 N 6865 7.00 C 25983 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.68 Conformation dependent library (CDL) restraints added in 8.1 seconds 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10842 Finding SS restraints... Secondary structure from input PDB file: 254 helices and 24 sheets defined 62.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.13 Creating SS restraints... Processing helix chain 'G' and resid 36 through 51 Processing helix chain 'G' and resid 53 through 72 removed outlier: 3.601A pdb=" N LYS G 57 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE G 71 " --> pdb=" O GLU G 67 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 101 removed outlier: 3.978A pdb=" N SER G 101 " --> pdb=" O GLU G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 115 removed outlier: 3.912A pdb=" N MET G 109 " --> pdb=" O ILE G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 132 Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 151 through 166 Processing helix chain 'G' and resid 178 through 194 Processing helix chain 'G' and resid 197 through 200 Processing helix chain 'G' and resid 201 through 216 Processing helix chain 'G' and resid 219 through 233 removed outlier: 3.563A pdb=" N THR G 223 " --> pdb=" O ASP G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 249 removed outlier: 8.202A pdb=" N LYS G 240 " --> pdb=" O THR G 236 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE G 241 " --> pdb=" O GLU G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 266 removed outlier: 3.916A pdb=" N LEU G 266 " --> pdb=" O TYR G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 282 Processing helix chain 'G' and resid 289 through 292 removed outlier: 3.609A pdb=" N GLU G 292 " --> pdb=" O VAL G 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 289 through 292' Processing helix chain 'G' and resid 293 through 305 Processing helix chain 'G' and resid 312 through 317 Processing helix chain 'G' and resid 322 through 343 Processing helix chain 'G' and resid 395 through 402 Processing helix chain 'G' and resid 403 through 414 Processing helix chain 'G' and resid 416 through 425 removed outlier: 4.702A pdb=" N VAL G 420 " --> pdb=" O CYS G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 427 through 433 Processing helix chain 'G' and resid 435 through 456 removed outlier: 3.553A pdb=" N ARG G 439 " --> pdb=" O GLU G 435 " (cutoff:3.500A) Proline residue: G 451 - end of helix Processing helix chain 'G' and resid 510 through 514 removed outlier: 3.563A pdb=" N SER G 513 " --> pdb=" O GLU G 510 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN G 514 " --> pdb=" O TRP G 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 510 through 514' Processing helix chain 'G' and resid 520 through 536 removed outlier: 4.379A pdb=" N ILE G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER G 533 " --> pdb=" O HIS G 529 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE G 534 " --> pdb=" O ILE G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 541 removed outlier: 4.008A pdb=" N GLY G 540 " --> pdb=" O PRO G 537 " (cutoff:3.500A) Processing helix chain 'G' and resid 542 through 560 removed outlier: 4.092A pdb=" N LEU G 546 " --> pdb=" O ILE G 542 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN G 560 " --> pdb=" O ASP G 556 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 580 removed outlier: 3.632A pdb=" N THR G 569 " --> pdb=" O SER G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 586 Processing helix chain 'G' and resid 591 through 603 removed outlier: 4.003A pdb=" N THR G 595 " --> pdb=" O ASN G 591 " (cutoff:3.500A) Processing helix chain 'G' and resid 606 through 620 Processing helix chain 'G' and resid 625 through 644 Processing helix chain 'G' and resid 650 through 665 removed outlier: 4.645A pdb=" N ARG G 656 " --> pdb=" O ALA G 652 " (cutoff:3.500A) Processing helix chain 'G' and resid 665 through 670 removed outlier: 3.563A pdb=" N SER G 669 " --> pdb=" O ASN G 665 " (cutoff:3.500A) Processing helix chain 'G' and resid 670 through 680 Processing helix chain 'G' and resid 682 through 691 Processing helix chain 'G' and resid 692 through 694 No H-bonds generated for 'chain 'G' and resid 692 through 694' Processing helix chain 'G' and resid 695 through 712 Processing helix chain 'G' and resid 727 through 742 Processing helix chain 'G' and resid 747 through 758 Processing helix chain 'G' and resid 759 through 761 No H-bonds generated for 'chain 'G' and resid 759 through 761' Processing helix chain 'G' and resid 762 through 776 removed outlier: 3.547A pdb=" N VAL G 766 " --> pdb=" O ASN G 762 " (cutoff:3.500A) Processing helix chain 'G' and resid 786 through 793 Processing helix chain 'G' and resid 796 through 807 Processing helix chain 'G' and resid 814 through 827 Processing helix chain 'G' and resid 830 through 847 removed outlier: 3.521A pdb=" N LEU G 843 " --> pdb=" O TYR G 839 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS G 844 " --> pdb=" O THR G 840 " (cutoff:3.500A) Processing helix chain 'G' and resid 851 through 877 removed outlier: 4.345A pdb=" N THR G 857 " --> pdb=" O LYS G 853 " (cutoff:3.500A) Processing helix chain 'G' and resid 878 through 885 removed outlier: 3.754A pdb=" N PHE G 882 " --> pdb=" O LYS G 878 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU G 883 " --> pdb=" O GLY G 879 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 895 Processing helix chain 'G' and resid 899 through 917 removed outlier: 5.653A pdb=" N ASP G 909 " --> pdb=" O HIS G 905 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR G 910 " --> pdb=" O ILE G 906 " (cutoff:3.500A) Processing helix chain 'G' and resid 941 through 951 removed outlier: 3.855A pdb=" N LEU G 951 " --> pdb=" O THR G 947 " (cutoff:3.500A) Processing helix chain 'G' and resid 960 through 970 removed outlier: 3.770A pdb=" N ASP G 964 " --> pdb=" O LYS G 960 " (cutoff:3.500A) Processing helix chain 'G' and resid 984 through 993 Processing helix chain 'G' and resid 993 through 1018 removed outlier: 4.062A pdb=" N GLY G 997 " --> pdb=" O ILE G 993 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU G1013 " --> pdb=" O GLU G1009 " (cutoff:3.500A) Processing helix chain 'G' and resid 1025 through 1034 removed outlier: 4.030A pdb=" N LEU G1031 " --> pdb=" O ILE G1027 " (cutoff:3.500A) Processing helix chain 'G' and resid 1035 through 1040 Processing helix chain 'G' and resid 1042 through 1054 removed outlier: 3.546A pdb=" N ALA G1046 " --> pdb=" O SER G1042 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE G1054 " --> pdb=" O SER G1050 " (cutoff:3.500A) Processing helix chain 'G' and resid 1058 through 1071 Processing helix chain 'G' and resid 1074 through 1082 removed outlier: 3.519A pdb=" N PHE G1080 " --> pdb=" O LYS G1076 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS G1082 " --> pdb=" O LEU G1078 " (cutoff:3.500A) Processing helix chain 'G' and resid 1083 through 1107 Processing helix chain 'G' and resid 1113 through 1133 Processing helix chain 'G' and resid 1137 through 1152 removed outlier: 4.015A pdb=" N ILE G1141 " --> pdb=" O ASN G1137 " (cutoff:3.500A) Processing helix chain 'G' and resid 1153 through 1155 No H-bonds generated for 'chain 'G' and resid 1153 through 1155' Processing helix chain 'H' and resid 3 through 22 removed outlier: 3.791A pdb=" N LEU H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 32 removed outlier: 3.960A pdb=" N HIS H 31 " --> pdb=" O ASP H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 39 removed outlier: 3.511A pdb=" N MET H 38 " --> pdb=" O PRO H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 47 removed outlier: 3.950A pdb=" N PHE H 46 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU H 47 " --> pdb=" O LEU H 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 43 through 47' Processing helix chain 'H' and resid 55 through 59 removed outlier: 3.647A pdb=" N HIS H 59 " --> pdb=" O SER H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 78 Processing helix chain 'H' and resid 91 through 106 removed outlier: 3.747A pdb=" N TYR H 104 " --> pdb=" O LEU H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 115 through 131 removed outlier: 3.551A pdb=" N LEU H 131 " --> pdb=" O ILE H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 147 Proline residue: H 142 - end of helix Processing helix chain 'H' and resid 147 through 152 removed outlier: 3.882A pdb=" N PHE H 151 " --> pdb=" O ARG H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 191 removed outlier: 4.346A pdb=" N LYS H 177 " --> pdb=" O PRO H 173 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG H 179 " --> pdb=" O TYR H 175 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN H 191 " --> pdb=" O LYS H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 214 removed outlier: 3.505A pdb=" N LEU H 214 " --> pdb=" O LEU H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 268 Processing helix chain 'H' and resid 271 through 275 Processing helix chain 'H' and resid 279 through 320 Proline residue: H 290 - end of helix Processing helix chain 'H' and resid 336 through 341 removed outlier: 3.671A pdb=" N HIS H 341 " --> pdb=" O VAL H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 343 through 361 Processing helix chain 'H' and resid 378 through 387 Processing helix chain 'H' and resid 392 through 416 removed outlier: 4.071A pdb=" N ASP H 416 " --> pdb=" O LEU H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 430 removed outlier: 3.667A pdb=" N PHE H 421 " --> pdb=" O GLU H 417 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU H 429 " --> pdb=" O CYS H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 442 through 456 Processing helix chain 'H' and resid 459 through 464 Processing helix chain 'H' and resid 470 through 491 removed outlier: 3.910A pdb=" N ASP H 491 " --> pdb=" O THR H 487 " (cutoff:3.500A) Processing helix chain 'H' and resid 493 through 497 removed outlier: 3.714A pdb=" N PHE H 496 " --> pdb=" O PHE H 493 " (cutoff:3.500A) Processing helix chain 'H' and resid 525 through 532 Processing helix chain 'H' and resid 577 through 587 Processing helix chain 'K' and resid 23 through 32 Processing helix chain 'K' and resid 42 through 53 Processing helix chain 'K' and resid 200 through 206 removed outlier: 3.694A pdb=" N ILE K 204 " --> pdb=" O ASN K 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 68 removed outlier: 3.520A pdb=" N LEU L 68 " --> pdb=" O LYS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 79 Processing helix chain 'L' and resid 86 through 97 Proline residue: L 94 - end of helix Processing helix chain 'L' and resid 111 through 124 removed outlier: 3.847A pdb=" N VAL L 115 " --> pdb=" O GLY L 111 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE L 116 " --> pdb=" O LYS L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 154 Processing helix chain 'L' and resid 170 through 180 Processing helix chain 'L' and resid 191 through 201 removed outlier: 3.595A pdb=" N GLU L 201 " --> pdb=" O ALA L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 223 Processing helix chain 'L' and resid 223 through 236 removed outlier: 3.577A pdb=" N ALA L 236 " --> pdb=" O GLU L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 289 through 291 No H-bonds generated for 'chain 'L' and resid 289 through 291' Processing helix chain 'L' and resid 292 through 304 removed outlier: 3.794A pdb=" N ASP L 302 " --> pdb=" O ALA L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 329 Processing helix chain 'L' and resid 341 through 354 Processing helix chain 'L' and resid 364 through 367 Processing helix chain 'L' and resid 386 through 395 Processing helix chain 'L' and resid 412 through 427 removed outlier: 3.970A pdb=" N GLN L 423 " --> pdb=" O LEU L 419 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU L 424 " --> pdb=" O ALA L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 439 through 443 Processing helix chain 'A' and resid 36 through 51 Processing helix chain 'A' and resid 53 through 72 removed outlier: 3.601A pdb=" N LYS A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 101 removed outlier: 3.979A pdb=" N SER A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.911A pdb=" N MET A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 151 through 166 Processing helix chain 'A' and resid 178 through 194 Processing helix chain 'A' and resid 197 through 200 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.564A pdb=" N THR A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 249 removed outlier: 8.204A pdb=" N LYS A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.916A pdb=" N LEU A 266 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 289 through 292 removed outlier: 3.609A pdb=" N GLU A 292 " --> pdb=" O VAL A 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 292' Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 322 through 343 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 414 Processing helix chain 'A' and resid 416 through 425 removed outlier: 4.703A pdb=" N VAL A 420 " --> pdb=" O CYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 433 Processing helix chain 'A' and resid 435 through 456 removed outlier: 3.553A pdb=" N ARG A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.564A pdb=" N SER A 513 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN A 514 " --> pdb=" O TRP A 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 510 through 514' Processing helix chain 'A' and resid 520 through 536 removed outlier: 4.380A pdb=" N ILE A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER A 533 " --> pdb=" O HIS A 529 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 4.008A pdb=" N GLY A 540 " --> pdb=" O PRO A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 560 removed outlier: 4.093A pdb=" N LEU A 546 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 580 removed outlier: 3.631A pdb=" N THR A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 591 through 603 removed outlier: 4.003A pdb=" N THR A 595 " --> pdb=" O ASN A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 620 Processing helix chain 'A' and resid 625 through 644 Processing helix chain 'A' and resid 650 through 665 removed outlier: 4.645A pdb=" N ARG A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.563A pdb=" N SER A 669 " --> pdb=" O ASN A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 680 Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 695 through 712 Processing helix chain 'A' and resid 727 through 742 Processing helix chain 'A' and resid 747 through 758 Processing helix chain 'A' and resid 759 through 761 No H-bonds generated for 'chain 'A' and resid 759 through 761' Processing helix chain 'A' and resid 762 through 776 removed outlier: 3.546A pdb=" N VAL A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 793 Processing helix chain 'A' and resid 796 through 807 Processing helix chain 'A' and resid 814 through 827 Processing helix chain 'A' and resid 830 through 847 removed outlier: 3.521A pdb=" N LEU A 843 " --> pdb=" O TYR A 839 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 877 removed outlier: 4.345A pdb=" N THR A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 885 removed outlier: 3.754A pdb=" N PHE A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU A 883 " --> pdb=" O GLY A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 895 Processing helix chain 'A' and resid 899 through 917 removed outlier: 5.652A pdb=" N ASP A 909 " --> pdb=" O HIS A 905 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR A 910 " --> pdb=" O ILE A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 951 removed outlier: 3.854A pdb=" N LEU A 951 " --> pdb=" O THR A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.771A pdb=" N ASP A 964 " --> pdb=" O LYS A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 993 Processing helix chain 'A' and resid 993 through 1018 removed outlier: 4.062A pdb=" N GLY A 997 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A1013 " --> pdb=" O GLU A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1034 removed outlier: 4.031A pdb=" N LEU A1031 " --> pdb=" O ILE A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1040 Processing helix chain 'A' and resid 1042 through 1054 removed outlier: 3.546A pdb=" N ALA A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1071 Processing helix chain 'A' and resid 1074 through 1082 removed outlier: 3.519A pdb=" N PHE A1080 " --> pdb=" O LYS A1076 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1107 Processing helix chain 'A' and resid 1113 through 1133 Processing helix chain 'A' and resid 1137 through 1152 removed outlier: 4.015A pdb=" N ILE A1141 " --> pdb=" O ASN A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1155 No H-bonds generated for 'chain 'A' and resid 1153 through 1155' Processing helix chain 'B' and resid 3 through 22 removed outlier: 3.791A pdb=" N LEU B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 32 removed outlier: 3.960A pdb=" N HIS B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 39 removed outlier: 3.511A pdb=" N MET B 38 " --> pdb=" O PRO B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.949A pdb=" N PHE B 46 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 47 " --> pdb=" O LEU B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 47' Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.647A pdb=" N HIS B 59 " --> pdb=" O SER B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 78 Processing helix chain 'B' and resid 91 through 106 removed outlier: 3.748A pdb=" N TYR B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 115 through 131 removed outlier: 3.551A pdb=" N LEU B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 Proline residue: B 142 - end of helix Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.881A pdb=" N PHE B 151 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 191 removed outlier: 4.346A pdb=" N LYS B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG B 179 " --> pdb=" O TYR B 175 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 214 removed outlier: 3.504A pdb=" N LEU B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 279 through 320 Proline residue: B 290 - end of helix Processing helix chain 'B' and resid 336 through 341 removed outlier: 3.671A pdb=" N HIS B 341 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 361 Processing helix chain 'B' and resid 378 through 387 Processing helix chain 'B' and resid 392 through 416 removed outlier: 4.071A pdb=" N ASP B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 430 removed outlier: 3.667A pdb=" N PHE B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 429 " --> pdb=" O CYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 456 Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 470 through 491 removed outlier: 3.909A pdb=" N ASP B 491 " --> pdb=" O THR B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 497 removed outlier: 3.713A pdb=" N PHE B 496 " --> pdb=" O PHE B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 532 Processing helix chain 'B' and resid 577 through 587 Processing helix chain 'E' and resid 23 through 32 Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 200 through 206 removed outlier: 3.694A pdb=" N ILE E 204 " --> pdb=" O ASN E 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 68 removed outlier: 3.519A pdb=" N LEU F 68 " --> pdb=" O LYS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 79 Processing helix chain 'F' and resid 86 through 97 Proline residue: F 94 - end of helix Processing helix chain 'F' and resid 111 through 124 removed outlier: 3.847A pdb=" N VAL F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 154 Processing helix chain 'F' and resid 170 through 180 Processing helix chain 'F' and resid 191 through 201 removed outlier: 3.595A pdb=" N GLU F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 223 Processing helix chain 'F' and resid 223 through 236 removed outlier: 3.576A pdb=" N ALA F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 291 No H-bonds generated for 'chain 'F' and resid 289 through 291' Processing helix chain 'F' and resid 292 through 304 removed outlier: 3.794A pdb=" N ASP F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 329 Processing helix chain 'F' and resid 341 through 354 Processing helix chain 'F' and resid 364 through 367 Processing helix chain 'F' and resid 386 through 395 Processing helix chain 'F' and resid 412 through 427 removed outlier: 3.969A pdb=" N GLN F 423 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F 424 " --> pdb=" O ALA F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'J' and resid 8 through 39 removed outlier: 3.679A pdb=" N GLU J 22 " --> pdb=" O GLN J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 84 Proline residue: J 55 - end of helix removed outlier: 4.491A pdb=" N GLU J 60 " --> pdb=" O ASP J 56 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE J 62 " --> pdb=" O HIS J 58 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN J 63 " --> pdb=" O ARG J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 91 removed outlier: 3.724A pdb=" N VAL J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 94 No H-bonds generated for 'chain 'J' and resid 92 through 94' Processing helix chain 'J' and resid 96 through 120 removed outlier: 3.932A pdb=" N ILE J 100 " --> pdb=" O ASN J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 159 removed outlier: 3.566A pdb=" N ILE J 156 " --> pdb=" O LYS J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 162 No H-bonds generated for 'chain 'J' and resid 160 through 162' Processing helix chain 'J' and resid 166 through 235 removed outlier: 3.635A pdb=" N VAL J 170 " --> pdb=" O ASP J 166 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 238 No H-bonds generated for 'chain 'J' and resid 237 through 238' Processing helix chain 'I' and resid 4 through 16 Processing helix chain 'I' and resid 21 through 44 removed outlier: 3.935A pdb=" N LEU I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 102 Processing helix chain 'I' and resid 103 through 105 No H-bonds generated for 'chain 'I' and resid 103 through 105' Processing helix chain 'I' and resid 106 through 143 Processing helix chain 'I' and resid 153 through 160 Processing helix chain 'I' and resid 163 through 169 removed outlier: 4.092A pdb=" N LEU I 167 " --> pdb=" O LEU I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 249 removed outlier: 3.831A pdb=" N SER I 239 " --> pdb=" O GLY I 235 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE I 240 " --> pdb=" O LYS I 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 39 removed outlier: 3.679A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 84 Proline residue: C 55 - end of helix removed outlier: 4.491A pdb=" N GLU C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE C 62 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN C 63 " --> pdb=" O ARG C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.724A pdb=" N VAL C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 96 through 120 removed outlier: 3.932A pdb=" N ILE C 100 " --> pdb=" O ASN C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 removed outlier: 3.566A pdb=" N ILE C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 166 through 194 removed outlier: 3.634A pdb=" N VAL C 170 " --> pdb=" O ASP C 166 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 235 removed outlier: 3.526A pdb=" N MET C 229 " --> pdb=" O ASP C 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 16 Processing helix chain 'D' and resid 21 through 44 removed outlier: 3.936A pdb=" N LEU D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 102 Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 106 through 143 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 163 through 169 removed outlier: 4.092A pdb=" N LEU D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 247 removed outlier: 3.659A pdb=" N ILE D 240 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 471 through 475 Processing sheet with id=AA2, first strand: chain 'G' and resid 484 through 485 removed outlier: 6.525A pdb=" N ARG G 484 " --> pdb=" O TYR J 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'G' and resid 487 through 491 removed outlier: 3.641A pdb=" N SER G 497 " --> pdb=" O TYR G 504 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 66 through 71 removed outlier: 6.722A pdb=" N SER K 81 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU K 69 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA K 79 " --> pdb=" O LEU K 69 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL K 101 " --> pdb=" O PHE K 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 117 through 119 removed outlier: 3.553A pdb=" N ASP K 117 " --> pdb=" O VAL K 131 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU K 141 " --> pdb=" O LYS K 151 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS K 151 " --> pdb=" O LEU K 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 163 through 168 removed outlier: 6.740A pdb=" N ALA K 178 " --> pdb=" O ASN K 164 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N CYS K 166 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU K 176 " --> pdb=" O CYS K 166 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR K 168 " --> pdb=" O TRP K 174 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP K 174 " --> pdb=" O TYR K 168 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP K 188 " --> pdb=" O SER K 195 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N SER K 195 " --> pdb=" O ASP K 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 214 through 217 removed outlier: 6.260A pdb=" N LYS K 237 " --> pdb=" O VAL K 245 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL K 245 " --> pdb=" O LYS K 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 256 through 261 removed outlier: 4.404A pdb=" N CYS K 277 " --> pdb=" O ILE K 291 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU K 289 " --> pdb=" O VAL K 279 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN K 281 " --> pdb=" O CYS K 287 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N CYS K 287 " --> pdb=" O ASN K 281 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 298 through 303 removed outlier: 3.549A pdb=" N THR K 300 " --> pdb=" O CYS K 313 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP K 323 " --> pdb=" O LEU K 329 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU K 329 " --> pdb=" O ASP K 323 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 344 through 346 Processing sheet with id=AB2, first strand: chain 'L' and resid 102 through 104 removed outlier: 6.135A pdb=" N VAL L 102 " --> pdb=" O MET L 245 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE L 212 " --> pdb=" O MET L 244 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE L 246 " --> pdb=" O PHE L 212 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE L 214 " --> pdb=" O PHE L 246 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL L 134 " --> pdb=" O VAL L 213 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ASP L 215 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE L 136 " --> pdb=" O ASP L 215 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA L 163 " --> pdb=" O VAL L 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 333 through 336 removed outlier: 6.208A pdb=" N VAL L 309 " --> pdb=" O CYS L 360 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N SER L 362 " --> pdb=" O VAL L 309 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE L 311 " --> pdb=" O SER L 362 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN L 308 " --> pdb=" O LEU L 377 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE L 379 " --> pdb=" O GLN L 308 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE L 310 " --> pdb=" O ILE L 379 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN L 282 " --> pdb=" O ALA L 406 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N SER L 408 " --> pdb=" O GLN L 282 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR L 284 " --> pdb=" O SER L 408 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL L 410 " --> pdb=" O TYR L 284 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE L 286 " --> pdb=" O VAL L 410 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA L 431 " --> pdb=" O GLN L 283 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR L 285 " --> pdb=" O ALA L 431 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 471 through 475 Processing sheet with id=AB5, first strand: chain 'A' and resid 484 through 485 removed outlier: 6.591A pdb=" N ARG A 484 " --> pdb=" O TYR C 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 487 through 491 removed outlier: 3.640A pdb=" N SER A 497 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 66 through 71 removed outlier: 6.722A pdb=" N SER E 81 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU E 69 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA E 79 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL E 101 " --> pdb=" O PHE E 91 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 117 through 119 removed outlier: 3.553A pdb=" N ASP E 117 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU E 141 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS E 151 " --> pdb=" O LEU E 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 163 through 168 removed outlier: 6.740A pdb=" N ALA E 178 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N CYS E 166 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU E 176 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR E 168 " --> pdb=" O TRP E 174 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP E 174 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP E 188 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N SER E 195 " --> pdb=" O ASP E 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 214 through 217 removed outlier: 6.260A pdb=" N LYS E 237 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL E 245 " --> pdb=" O LYS E 237 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 256 through 261 removed outlier: 4.403A pdb=" N CYS E 277 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 289 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN E 281 " --> pdb=" O CYS E 287 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N CYS E 287 " --> pdb=" O ASN E 281 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 298 through 303 removed outlier: 3.547A pdb=" N THR E 300 " --> pdb=" O CYS E 313 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP E 323 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU E 329 " --> pdb=" O ASP E 323 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 344 through 346 Processing sheet with id=AC5, first strand: chain 'F' and resid 102 through 104 removed outlier: 6.135A pdb=" N VAL F 102 " --> pdb=" O MET F 245 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE F 212 " --> pdb=" O MET F 244 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE F 246 " --> pdb=" O PHE F 212 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE F 214 " --> pdb=" O PHE F 246 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL F 134 " --> pdb=" O VAL F 213 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASP F 215 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE F 136 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA F 163 " --> pdb=" O VAL F 189 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 333 through 336 removed outlier: 6.208A pdb=" N VAL F 309 " --> pdb=" O CYS F 360 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N SER F 362 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ILE F 311 " --> pdb=" O SER F 362 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN F 308 " --> pdb=" O LEU F 377 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE F 379 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE F 310 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN F 282 " --> pdb=" O ALA F 406 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N SER F 408 " --> pdb=" O GLN F 282 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR F 284 " --> pdb=" O SER F 408 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL F 410 " --> pdb=" O TYR F 284 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE F 286 " --> pdb=" O VAL F 410 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA F 431 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR F 285 " --> pdb=" O ALA F 431 " (cutoff:3.500A) 2506 hydrogen bonds defined for protein. 7374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.45 Time building geometry restraints manager: 15.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6536 1.30 - 1.43: 10737 1.43 - 1.56: 23585 1.56 - 1.68: 0 1.68 - 1.81: 210 Bond restraints: 41068 Sorted by residual: bond pdb=" C LYS D 236 " pdb=" O LYS D 236 " ideal model delta sigma weight residual 1.236 1.322 -0.085 1.15e-02 7.56e+03 5.51e+01 bond pdb=" C ARG D 229 " pdb=" O ARG D 229 " ideal model delta sigma weight residual 1.236 1.318 -0.081 1.15e-02 7.56e+03 4.98e+01 bond pdb=" C ILE D 233 " pdb=" O ILE D 233 " ideal model delta sigma weight residual 1.237 1.315 -0.078 1.17e-02 7.31e+03 4.39e+01 bond pdb=" C LYS I 236 " pdb=" O LYS I 236 " ideal model delta sigma weight residual 1.237 1.304 -0.067 1.19e-02 7.06e+03 3.21e+01 bond pdb=" C TYR C 194 " pdb=" O TYR C 194 " ideal model delta sigma weight residual 1.235 1.306 -0.070 1.26e-02 6.30e+03 3.12e+01 ... (remaining 41063 not shown) Histogram of bond angle deviations from ideal: 95.40 - 103.15: 320 103.15 - 110.91: 15528 110.91 - 118.66: 17815 118.66 - 126.41: 21951 126.41 - 134.17: 500 Bond angle restraints: 56114 Sorted by residual: angle pdb=" C THR I 81 " pdb=" CA THR I 81 " pdb=" CB THR I 81 " ideal model delta sigma weight residual 110.88 95.40 15.48 1.57e+00 4.06e-01 9.72e+01 angle pdb=" C THR D 81 " pdb=" CA THR D 81 " pdb=" CB THR D 81 " ideal model delta sigma weight residual 110.88 95.47 15.41 1.57e+00 4.06e-01 9.64e+01 angle pdb=" N ASN G 36 " pdb=" CA ASN G 36 " pdb=" C ASN G 36 " ideal model delta sigma weight residual 112.58 103.26 9.32 1.22e+00 6.72e-01 5.84e+01 angle pdb=" N ASN A 36 " pdb=" CA ASN A 36 " pdb=" C ASN A 36 " ideal model delta sigma weight residual 112.58 103.28 9.30 1.22e+00 6.72e-01 5.81e+01 angle pdb=" C THR C 114 " pdb=" CA THR C 114 " pdb=" CB THR C 114 " ideal model delta sigma weight residual 110.79 99.80 10.99 1.66e+00 3.63e-01 4.39e+01 ... (remaining 56109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 21463 17.91 - 35.83: 2091 35.83 - 53.74: 624 53.74 - 71.65: 92 71.65 - 89.57: 30 Dihedral angle restraints: 24300 sinusoidal: 7676 harmonic: 16624 Sorted by residual: dihedral pdb=" C THR I 81 " pdb=" N THR I 81 " pdb=" CA THR I 81 " pdb=" CB THR I 81 " ideal model delta harmonic sigma weight residual -122.00 -104.62 -17.38 0 2.50e+00 1.60e-01 4.83e+01 dihedral pdb=" C THR D 81 " pdb=" N THR D 81 " pdb=" CA THR D 81 " pdb=" CB THR D 81 " ideal model delta harmonic sigma weight residual -122.00 -104.75 -17.25 0 2.50e+00 1.60e-01 4.76e+01 dihedral pdb=" CA PHE G 932 " pdb=" C PHE G 932 " pdb=" N SER G 933 " pdb=" CA SER G 933 " ideal model delta harmonic sigma weight residual -180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 24297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 5794 0.083 - 0.167: 746 0.167 - 0.250: 193 0.250 - 0.333: 26 0.333 - 0.417: 10 Chirality restraints: 6769 Sorted by residual: chirality pdb=" CA ILE J 66 " pdb=" N ILE J 66 " pdb=" C ILE J 66 " pdb=" CB ILE J 66 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA ILE C 66 " pdb=" N ILE C 66 " pdb=" C ILE C 66 " pdb=" CB ILE C 66 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA THR I 81 " pdb=" N THR I 81 " pdb=" C THR I 81 " pdb=" CB THR I 81 " both_signs ideal model delta sigma weight residual False 2.53 2.90 -0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 6766 not shown) Planarity restraints: 7146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN I 206 " -0.031 2.00e-02 2.50e+03 6.14e-02 3.77e+01 pdb=" C ASN I 206 " 0.106 2.00e-02 2.50e+03 pdb=" O ASN I 206 " -0.039 2.00e-02 2.50e+03 pdb=" N ALA I 207 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 46 " -0.027 2.00e-02 2.50e+03 5.51e-02 3.04e+01 pdb=" C LEU C 46 " 0.095 2.00e-02 2.50e+03 pdb=" O LEU C 46 " -0.035 2.00e-02 2.50e+03 pdb=" N ALEU C 47 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU J 46 " -0.027 2.00e-02 2.50e+03 5.50e-02 3.02e+01 pdb=" C LEU J 46 " 0.095 2.00e-02 2.50e+03 pdb=" O LEU J 46 " -0.035 2.00e-02 2.50e+03 pdb=" N ALEU J 47 " -0.033 2.00e-02 2.50e+03 ... (remaining 7143 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 35 2.22 - 2.89: 17012 2.89 - 3.56: 57862 3.56 - 4.23: 82676 4.23 - 4.90: 143721 Nonbonded interactions: 301306 Sorted by model distance: nonbonded pdb=" CB THR D 151 " pdb=" CB TRP D 155 " model vdw 1.547 3.870 nonbonded pdb=" CB THR I 151 " pdb=" CB TRP I 155 " model vdw 1.548 3.870 nonbonded pdb=" O ARG C 67 " pdb=" OD1 ASP C 71 " model vdw 1.577 3.040 nonbonded pdb=" O ARG J 67 " pdb=" OD1 ASP J 71 " model vdw 1.578 3.040 nonbonded pdb=" O LEU G 524 " pdb=" OG SER G 528 " model vdw 2.091 2.440 ... (remaining 301301 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 'G' } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = (chain 'C' and (resid 6 through 46 or resid 48 through 235)) selection = (chain 'J' and (resid 6 through 46 or resid 48 through 235)) } ncs_group { reference = chain 'D' selection = (chain 'I' and resid 2 through 247) } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 7.500 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 103.150 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4869 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 : 0.008 0.085 41068 Z= 0.520 Angle : 1.019 15.480 56114 Z= 0.715 Chirality : 0.065 0.417 6769 Planarity : 0.006 0.061 7146 Dihedral : 16.269 89.567 13458 Min Nonbonded Distance : 1.547 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.18 % Favored : 93.59 % Rotamer: Outliers : 10.45 % Allowed : 19.19 % Favored : 70.36 % Cbeta Deviations : 0.30 % 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: -1.71 (0.11), residues: 5543 helix: -0.15 (0.09), residues: 3197 sheet: -1.05 (0.23), residues: 462 loop : -2.85 (0.12), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP J 147 HIS 0.005 0.001 HIS G 414 PHE 0.029 0.002 PHE G 694 TYR 0.022 0.002 TYR D 17 ARG 0.005 0.001 ARG J 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 373 poor density : 335 time to evaluate : 4.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 MET cc_start: 0.3309 (mtt) cc_final: 0.2185 (mtt) REVERT: G 285 TYR cc_start: -0.0111 (OUTLIER) cc_final: -0.0984 (t80) REVERT: G 411 LEU cc_start: -0.1254 (OUTLIER) cc_final: -0.1607 (tp) REVERT: G 552 ILE cc_start: -0.1594 (OUTLIER) cc_final: -0.2304 (mt) REVERT: G 711 THR cc_start: 0.0406 (OUTLIER) cc_final: -0.0021 (p) REVERT: G 724 GLN cc_start: 0.0482 (OUTLIER) cc_final: -0.0075 (mp10) REVERT: G 790 LEU cc_start: 0.4807 (tt) cc_final: 0.4536 (tp) REVERT: G 842 ASN cc_start: -0.4349 (OUTLIER) cc_final: -0.5508 (t0) REVERT: G 1036 VAL cc_start: 0.5015 (OUTLIER) cc_final: 0.4811 (t) REVERT: G 1081 CYS cc_start: 0.0228 (t) cc_final: -0.0216 (p) REVERT: G 1151 VAL cc_start: 0.3707 (p) cc_final: 0.3422 (m) REVERT: H 376 LEU cc_start: 0.3817 (OUTLIER) cc_final: 0.3601 (pt) REVERT: H 443 VAL cc_start: 0.2271 (OUTLIER) cc_final: 0.1273 (t) REVERT: H 479 MET cc_start: 0.0509 (mtm) cc_final: -0.0212 (mtt) REVERT: L 227 ARG cc_start: 0.4240 (ptm160) cc_final: 0.4021 (ptm160) REVERT: L 244 MET cc_start: 0.2249 (mpp) cc_final: 0.0495 (mpp) REVERT: L 245 MET cc_start: 0.2865 (mmt) cc_final: 0.2583 (mmt) REVERT: L 307 ASN cc_start: 0.6482 (m-40) cc_final: 0.5067 (m110) REVERT: A 136 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7672 (t70) REVERT: A 137 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8730 (pm20) REVERT: A 138 GLU cc_start: 0.8078 (tp30) cc_final: 0.7782 (tm-30) REVERT: A 154 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6886 (mm-40) REVERT: A 217 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8170 (t) REVERT: A 300 MET cc_start: 0.8726 (ttp) cc_final: 0.8472 (tmm) REVERT: A 323 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8604 (tpp) REVERT: A 572 LYS cc_start: 0.9560 (OUTLIER) cc_final: 0.9347 (ttmt) REVERT: A 619 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8983 (t) REVERT: A 738 LEU cc_start: 0.8890 (mt) cc_final: 0.8604 (tp) REVERT: A 745 MET cc_start: 0.8000 (tpp) cc_final: 0.7767 (tpt) REVERT: A 747 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8998 (mm) REVERT: A 1092 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8840 (tt) REVERT: A 1148 MET cc_start: 0.9107 (mmm) cc_final: 0.8874 (mmm) REVERT: B 196 THR cc_start: 0.9448 (OUTLIER) cc_final: 0.9223 (t) REVERT: B 278 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7745 (mt) REVERT: B 371 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9117 (tp) REVERT: B 528 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8582 (mt) REVERT: F 284 TYR cc_start: 0.7800 (m-80) cc_final: 0.7334 (m-80) REVERT: F 326 LEU cc_start: 0.9484 (tp) cc_final: 0.9273 (tt) REVERT: F 339 HIS cc_start: 0.9306 (t-170) cc_final: 0.9062 (m90) REVERT: C 156 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8339 (mm) REVERT: C 178 LEU cc_start: 0.9152 (mt) cc_final: 0.8730 (tp) REVERT: D 107 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8926 (tt) REVERT: D 133 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8353 (p) outliers start: 373 outliers final: 65 residues processed: 685 average time/residue: 0.4610 time to fit residues: 534.6114 Evaluate side-chains 300 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 210 time to evaluate : 4.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 468 optimal weight: 7.9990 chunk 420 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 283 optimal weight: 4.9990 chunk 224 optimal weight: 40.0000 chunk 435 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 264 optimal weight: 6.9990 chunk 323 optimal weight: 9.9990 chunk 504 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 102 GLN G 154 GLN ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 414 HIS G 422 HIS G 529 HIS G 703 GLN G 744 ASN G 759 HIS G 794 ASN G 893 ASN G1032 GLN G1150 HIS ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 180 HIS H 221 ASN H 282 ASN H 385 GLN H 397 GLN H 401 GLN K 143 ASN K 281 ASN K 325 ASN L 122 GLN L 123 GLN ** L 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 380 ASN L 385 ASN A 102 GLN A 154 GLN A 318 ASN A 414 HIS A 487 HIS A 529 HIS A 615 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN A 893 ASN A1032 GLN A1033 ASN A1150 HIS ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 HIS B 221 ASN B 282 ASN B 350 ASN B 385 GLN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 HIS F 122 GLN ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN F 385 ASN J 79 GLN J 109 HIS J 180 GLN I 25 ASN C 74 GLN C 79 GLN C 109 HIS ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 GLN D 25 ASN D 93 GLN D 94 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5191 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 41068 Z= 0.390 Angle : 0.773 10.938 56114 Z= 0.406 Chirality : 0.046 0.304 6769 Planarity : 0.005 0.068 7146 Dihedral : 4.991 23.424 5930 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 0.31 % Allowed : 5.80 % Favored : 93.89 % 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: -0.59 (0.11), residues: 5543 helix: 0.59 (0.09), residues: 3236 sheet: -0.51 (0.24), residues: 482 loop : -2.12 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 949 HIS 0.010 0.002 HIS J 58 PHE 0.042 0.003 PHE A 632 TYR 0.026 0.002 TYR A 839 ARG 0.013 0.001 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 226 time to evaluate : 5.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 MET cc_start: 0.2973 (mtt) cc_final: 0.2263 (mtt) REVERT: G 862 MET cc_start: 0.1498 (tpp) cc_final: 0.0337 (ptt) REVERT: G 1081 CYS cc_start: 0.0230 (t) cc_final: -0.0160 (p) REVERT: H 339 MET cc_start: 0.7427 (mpp) cc_final: 0.6697 (mpp) REVERT: H 479 MET cc_start: -0.0741 (mtm) cc_final: -0.2130 (mtt) REVERT: K 261 MET cc_start: 0.2285 (ttm) cc_final: 0.1930 (ttt) REVERT: L 157 MET cc_start: 0.4579 (mtm) cc_final: 0.3722 (mmm) REVERT: A 135 LEU cc_start: 0.9157 (pt) cc_final: 0.8506 (pt) REVERT: A 300 MET cc_start: 0.8786 (ttp) cc_final: 0.8258 (tmm) REVERT: A 745 MET cc_start: 0.8282 (tpp) cc_final: 0.8021 (tpp) REVERT: A 1055 MET cc_start: 0.8449 (tmm) cc_final: 0.8217 (tmm) REVERT: B 122 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7619 (tm-30) REVERT: B 372 MET cc_start: 0.8195 (mmm) cc_final: 0.7648 (mmm) REVERT: E 355 MET cc_start: 0.8847 (ttp) cc_final: 0.8577 (ptm) REVERT: F 310 ILE cc_start: 0.9096 (mt) cc_final: 0.8886 (tp) REVERT: I 109 ASP cc_start: 0.6405 (p0) cc_final: 0.6120 (p0) REVERT: C 178 LEU cc_start: 0.9415 (mt) cc_final: 0.9180 (tp) outliers start: 11 outliers final: 4 residues processed: 237 average time/residue: 0.4884 time to fit residues: 200.8761 Evaluate side-chains 171 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 4.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 280 optimal weight: 0.9990 chunk 156 optimal weight: 30.0000 chunk 419 optimal weight: 4.9990 chunk 343 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 504 optimal weight: 7.9990 chunk 545 optimal weight: 0.8980 chunk 449 optimal weight: 20.0000 chunk 500 optimal weight: 30.0000 chunk 172 optimal weight: 30.0000 chunk 405 optimal weight: 0.6980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 154 GLN ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 HIS G 744 ASN G1032 GLN G1033 ASN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 223 ASN H 260 ASN H 341 HIS K 219 ASN L 91 HIS ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN A 331 GLN A 615 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 ASN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 HIS ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 HIS J 21 GLN D 93 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5159 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41068 Z= 0.217 Angle : 0.575 11.433 56114 Z= 0.304 Chirality : 0.041 0.199 6769 Planarity : 0.004 0.048 7146 Dihedral : 4.358 20.029 5930 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 0.08 % Allowed : 3.98 % Favored : 95.94 % 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: 0.25 (0.11), residues: 5543 helix: 1.32 (0.09), residues: 3219 sheet: -0.11 (0.24), residues: 490 loop : -1.88 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 147 HIS 0.011 0.001 HIS G1000 PHE 0.018 0.001 PHE G 110 TYR 0.026 0.001 TYR F 349 ARG 0.007 0.000 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 209 time to evaluate : 4.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 862 MET cc_start: 0.1397 (tpp) cc_final: -0.0012 (ptt) REVERT: G 1081 CYS cc_start: -0.0371 (t) cc_final: -0.0611 (p) REVERT: H 479 MET cc_start: -0.0517 (mtm) cc_final: -0.2084 (mtt) REVERT: K 261 MET cc_start: 0.1897 (ttm) cc_final: 0.1257 (ttp) REVERT: L 157 MET cc_start: 0.4706 (mtm) cc_final: 0.3754 (mmm) REVERT: L 245 MET cc_start: 0.2429 (mmt) cc_final: 0.1550 (ptp) REVERT: A 225 ASP cc_start: 0.9211 (t0) cc_final: 0.8971 (t70) REVERT: B 372 MET cc_start: 0.8281 (mmm) cc_final: 0.7666 (mmm) REVERT: E 355 MET cc_start: 0.8776 (ttp) cc_final: 0.8317 (ptm) REVERT: F 339 HIS cc_start: 0.9266 (t70) cc_final: 0.8829 (m90) REVERT: D 25 ASN cc_start: 0.8936 (m-40) cc_final: 0.8658 (m110) outliers start: 3 outliers final: 1 residues processed: 212 average time/residue: 0.4730 time to fit residues: 176.9942 Evaluate side-chains 167 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 4.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 498 optimal weight: 20.0000 chunk 379 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 55 optimal weight: 40.0000 chunk 240 optimal weight: 0.0870 chunk 339 optimal weight: 9.9990 chunk 506 optimal weight: 50.0000 chunk 536 optimal weight: 10.0000 chunk 264 optimal weight: 0.6980 chunk 480 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 overall best weight: 4.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 102 GLN G 136 HIS ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 ASN ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 703 GLN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 223 HIS A 331 GLN A 615 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 HIS F 123 GLN ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 GLN I 16 HIS ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5272 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 41068 Z= 0.306 Angle : 0.641 8.501 56114 Z= 0.338 Chirality : 0.042 0.220 6769 Planarity : 0.004 0.056 7146 Dihedral : 4.499 21.251 5930 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.53 % 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: 0.27 (0.11), residues: 5543 helix: 1.25 (0.09), residues: 3258 sheet: 0.02 (0.24), residues: 480 loop : -1.78 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 147 HIS 0.006 0.001 HIS B 265 PHE 0.050 0.002 PHE A 632 TYR 0.027 0.002 TYR F 349 ARG 0.012 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 4.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 862 MET cc_start: 0.0943 (tpp) cc_final: -0.0745 (ptt) REVERT: H 372 MET cc_start: 0.3364 (pmm) cc_final: 0.3029 (pmm) REVERT: H 479 MET cc_start: -0.1365 (mtm) cc_final: -0.3180 (mtt) REVERT: K 261 MET cc_start: 0.2215 (ttm) cc_final: 0.1742 (ttm) REVERT: L 245 MET cc_start: 0.2654 (mmt) cc_final: 0.1505 (ptt) REVERT: A 225 ASP cc_start: 0.9122 (t0) cc_final: 0.8913 (t70) REVERT: A 300 MET cc_start: 0.8418 (tmm) cc_final: 0.8170 (tmm) REVERT: A 787 MET cc_start: 0.8968 (tpp) cc_final: 0.8651 (tpp) REVERT: B 38 MET cc_start: 0.7656 (tpt) cc_final: 0.7428 (tpt) REVERT: B 122 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7587 (tm-30) REVERT: E 355 MET cc_start: 0.8788 (ttp) cc_final: 0.8273 (ptm) outliers start: 3 outliers final: 1 residues processed: 192 average time/residue: 0.4441 time to fit residues: 152.5513 Evaluate side-chains 158 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 4.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 446 optimal weight: 7.9990 chunk 304 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 399 optimal weight: 6.9990 chunk 221 optimal weight: 0.6980 chunk 457 optimal weight: 10.0000 chunk 370 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 273 optimal weight: 10.0000 chunk 481 optimal weight: 30.0000 chunk 135 optimal weight: 30.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 426 GLN ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 260 ASN L 123 GLN A 487 HIS A 615 ASN A 703 GLN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5262 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 41068 Z= 0.242 Angle : 0.572 7.381 56114 Z= 0.301 Chirality : 0.041 0.390 6769 Planarity : 0.004 0.058 7146 Dihedral : 4.283 19.938 5930 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.12), residues: 5543 helix: 1.54 (0.09), residues: 3250 sheet: 0.16 (0.24), residues: 486 loop : -1.67 (0.15), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 280 HIS 0.012 0.001 HIS G1000 PHE 0.025 0.001 PHE A 110 TYR 0.021 0.002 TYR F 349 ARG 0.009 0.000 ARG F 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 187 time to evaluate : 4.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 862 MET cc_start: 0.0795 (tpp) cc_final: -0.0807 (ptt) REVERT: H 38 MET cc_start: -0.0629 (mtp) cc_final: -0.1821 (mtp) REVERT: H 372 MET cc_start: 0.3960 (pmm) cc_final: 0.3523 (pmm) REVERT: H 479 MET cc_start: -0.1278 (mtm) cc_final: -0.3194 (mtt) REVERT: K 261 MET cc_start: 0.2393 (ttm) cc_final: 0.2090 (ttm) REVERT: L 245 MET cc_start: 0.2364 (mmt) cc_final: 0.1573 (ptt) REVERT: A 787 MET cc_start: 0.8820 (tpp) cc_final: 0.8466 (tpp) REVERT: B 38 MET cc_start: 0.7592 (tpt) cc_final: 0.7305 (tpt) REVERT: B 122 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7484 (tm-30) REVERT: B 523 MET cc_start: 0.8712 (mtp) cc_final: 0.8212 (ptp) REVERT: E 355 MET cc_start: 0.8737 (ttp) cc_final: 0.8204 (ptm) outliers start: 2 outliers final: 0 residues processed: 189 average time/residue: 0.4585 time to fit residues: 155.1365 Evaluate side-chains 158 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 4.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 180 optimal weight: 50.0000 chunk 483 optimal weight: 20.0000 chunk 106 optimal weight: 30.0000 chunk 314 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 536 optimal weight: 10.0000 chunk 445 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 177 optimal weight: 20.0000 chunk 281 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 271 ASN G 281 ASN ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN ** H 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 325 ASN A 233 GLN A 615 ASN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 HIS ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 ASN I 93 GLN C 74 GLN ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5376 moved from start: 0.6980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 41068 Z= 0.407 Angle : 0.727 10.852 56114 Z= 0.383 Chirality : 0.044 0.225 6769 Planarity : 0.004 0.062 7146 Dihedral : 4.879 24.407 5930 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.11), residues: 5543 helix: 1.00 (0.09), residues: 3261 sheet: -0.05 (0.25), residues: 476 loop : -1.74 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 532 HIS 0.007 0.001 HIS G 160 PHE 0.066 0.002 PHE A 632 TYR 0.031 0.002 TYR C 103 ARG 0.019 0.001 ARG G 811 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 4.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 862 MET cc_start: 0.0871 (tpp) cc_final: -0.0982 (ptt) REVERT: G 1085 SER cc_start: 0.7078 (m) cc_final: 0.6387 (p) REVERT: H 38 MET cc_start: -0.0231 (mtp) cc_final: -0.1530 (mtp) REVERT: H 372 MET cc_start: 0.3648 (pmm) cc_final: 0.3161 (pmm) REVERT: H 479 MET cc_start: -0.1295 (mtm) cc_final: -0.3214 (mtt) REVERT: A 300 MET cc_start: 0.8544 (tmm) cc_final: 0.8313 (tmm) REVERT: B 38 MET cc_start: 0.7835 (tpt) cc_final: 0.7551 (tpt) REVERT: B 122 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 345 MET cc_start: 0.9102 (mmp) cc_final: 0.8822 (mmm) REVERT: B 523 MET cc_start: 0.8804 (mtp) cc_final: 0.8462 (mtm) outliers start: 1 outliers final: 1 residues processed: 186 average time/residue: 0.4292 time to fit residues: 142.2592 Evaluate side-chains 159 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 517 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 305 optimal weight: 5.9990 chunk 392 optimal weight: 2.9990 chunk 303 optimal weight: 0.9980 chunk 452 optimal weight: 0.9990 chunk 299 optimal weight: 1.9990 chunk 534 optimal weight: 7.9990 chunk 334 optimal weight: 0.7980 chunk 326 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 HIS A 615 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN C 74 GLN D 16 HIS D 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5235 moved from start: 0.6969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 41068 Z= 0.144 Angle : 0.534 8.509 56114 Z= 0.280 Chirality : 0.040 0.195 6769 Planarity : 0.003 0.061 7146 Dihedral : 4.185 24.109 5930 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.97 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 0.75 (0.12), residues: 5543 helix: 1.66 (0.09), residues: 3254 sheet: 0.21 (0.25), residues: 476 loop : -1.62 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 532 HIS 0.004 0.001 HIS A 136 PHE 0.023 0.001 PHE A 110 TYR 0.024 0.001 TYR B 472 ARG 0.006 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 4.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 109 MET cc_start: 0.0454 (ttm) cc_final: 0.0020 (tpp) REVERT: G 602 MET cc_start: -0.1754 (tpt) cc_final: -0.2072 (tpt) REVERT: G 862 MET cc_start: 0.0657 (tpp) cc_final: -0.0948 (ptt) REVERT: G 1148 MET cc_start: 0.2306 (ppp) cc_final: 0.0776 (mmm) REVERT: H 38 MET cc_start: -0.0184 (mtp) cc_final: -0.1381 (mtp) REVERT: H 372 MET cc_start: 0.3510 (pmm) cc_final: 0.3223 (pmm) REVERT: H 479 MET cc_start: -0.1389 (mtm) cc_final: -0.3240 (mtt) REVERT: K 261 MET cc_start: 0.2705 (ttm) cc_final: 0.1560 (ttp) REVERT: L 244 MET cc_start: 0.3002 (mpp) cc_final: 0.2469 (mpp) REVERT: L 245 MET cc_start: 0.2065 (mmt) cc_final: 0.1415 (ptt) REVERT: B 38 MET cc_start: 0.7522 (tpt) cc_final: 0.7303 (tpt) REVERT: B 523 MET cc_start: 0.8775 (mtp) cc_final: 0.8249 (mtm) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.4597 time to fit residues: 154.3432 Evaluate side-chains 159 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 4.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 330 optimal weight: 0.9980 chunk 213 optimal weight: 30.0000 chunk 319 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 340 optimal weight: 9.9990 chunk 364 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 420 optimal weight: 8.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN ** H 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS A 615 ASN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN F 380 ASN I 94 GLN ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5371 moved from start: 0.7555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 41068 Z= 0.349 Angle : 0.667 10.630 56114 Z= 0.351 Chirality : 0.043 0.227 6769 Planarity : 0.004 0.062 7146 Dihedral : 4.639 24.748 5930 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 0.03 % Allowed : 1.15 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.12), residues: 5543 helix: 1.33 (0.09), residues: 3249 sheet: 0.03 (0.24), residues: 488 loop : -1.62 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 532 HIS 0.006 0.001 HIS G 160 PHE 0.037 0.002 PHE A 632 TYR 0.024 0.002 TYR F 349 ARG 0.007 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 4.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 298 MET cc_start: -0.4180 (tmm) cc_final: -0.5009 (ttp) REVERT: G 465 MET cc_start: -0.2782 (tpt) cc_final: -0.3257 (tpp) REVERT: G 862 MET cc_start: 0.0581 (tpp) cc_final: -0.1211 (ptt) REVERT: G 1081 CYS cc_start: -0.0357 (t) cc_final: -0.1631 (p) REVERT: G 1148 MET cc_start: 0.2641 (ppp) cc_final: 0.0743 (mmm) REVERT: H 38 MET cc_start: -0.0521 (mtp) cc_final: -0.1704 (mtp) REVERT: H 372 MET cc_start: 0.3255 (pmm) cc_final: 0.2734 (pmm) REVERT: H 479 MET cc_start: -0.1149 (mtm) cc_final: -0.3007 (mtt) REVERT: K 261 MET cc_start: 0.3289 (ttm) cc_final: 0.2703 (ttm) REVERT: L 244 MET cc_start: 0.3146 (mpp) cc_final: 0.2577 (mpp) REVERT: L 245 MET cc_start: 0.1884 (mmt) cc_final: 0.1218 (ptp) REVERT: A 300 MET cc_start: 0.8567 (tmm) cc_final: 0.8356 (tmm) REVERT: A 1055 MET cc_start: 0.8391 (ttm) cc_final: 0.8111 (tmm) REVERT: B 77 MET cc_start: 0.8894 (mmm) cc_final: 0.8316 (mmm) REVERT: B 523 MET cc_start: 0.8783 (mtp) cc_final: 0.8516 (mtm) outliers start: 1 outliers final: 1 residues processed: 183 average time/residue: 0.4686 time to fit residues: 151.1322 Evaluate side-chains 157 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 4.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 486 optimal weight: 50.0000 chunk 512 optimal weight: 3.9990 chunk 467 optimal weight: 50.0000 chunk 498 optimal weight: 10.0000 chunk 300 optimal weight: 0.6980 chunk 217 optimal weight: 20.0000 chunk 391 optimal weight: 0.1980 chunk 152 optimal weight: 5.9990 chunk 450 optimal weight: 6.9990 chunk 471 optimal weight: 40.0000 chunk 496 optimal weight: 20.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5333 moved from start: 0.7779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 41068 Z= 0.238 Angle : 0.579 7.758 56114 Z= 0.304 Chirality : 0.041 0.197 6769 Planarity : 0.004 0.061 7146 Dihedral : 4.404 24.428 5930 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.07 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 0.66 (0.12), residues: 5543 helix: 1.58 (0.09), residues: 3241 sheet: -0.15 (0.25), residues: 458 loop : -1.51 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1018 HIS 0.004 0.001 HIS F 337 PHE 0.030 0.001 PHE C 107 TYR 0.021 0.001 TYR F 349 ARG 0.007 0.000 ARG F 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 4.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 MET cc_start: 0.2435 (ttt) cc_final: 0.1791 (ttt) REVERT: G 298 MET cc_start: -0.4562 (tmm) cc_final: -0.5641 (ttp) REVERT: G 465 MET cc_start: -0.2783 (tpt) cc_final: -0.3247 (tpp) REVERT: G 862 MET cc_start: 0.0603 (tpp) cc_final: -0.1112 (ptt) REVERT: G 1081 CYS cc_start: -0.0302 (t) cc_final: -0.1514 (p) REVERT: G 1148 MET cc_start: 0.2796 (ppp) cc_final: 0.0949 (mmm) REVERT: H 38 MET cc_start: -0.0423 (mtp) cc_final: -0.1443 (mtp) REVERT: H 372 MET cc_start: 0.3157 (pmm) cc_final: 0.2657 (pmm) REVERT: H 479 MET cc_start: -0.1221 (mtm) cc_final: -0.2884 (mtt) REVERT: H 541 ILE cc_start: 0.5067 (mm) cc_final: 0.4474 (mm) REVERT: K 261 MET cc_start: 0.2803 (ttm) cc_final: 0.2235 (ttm) REVERT: L 244 MET cc_start: 0.3083 (mpp) cc_final: 0.2508 (mpp) REVERT: L 245 MET cc_start: 0.1894 (mmt) cc_final: 0.1302 (ptp) REVERT: B 38 MET cc_start: 0.8170 (tpt) cc_final: 0.7932 (tpt) REVERT: B 523 MET cc_start: 0.8803 (mtp) cc_final: 0.8364 (mtm) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.4614 time to fit residues: 145.9298 Evaluate side-chains 152 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 327 optimal weight: 8.9990 chunk 527 optimal weight: 2.9990 chunk 321 optimal weight: 0.8980 chunk 250 optimal weight: 3.9990 chunk 366 optimal weight: 0.9980 chunk 552 optimal weight: 9.9990 chunk 508 optimal weight: 9.9990 chunk 440 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 340 optimal weight: 9.9990 chunk 269 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN H 221 ASN K 252 HIS ** L 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5267 moved from start: 0.7854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 41068 Z= 0.150 Angle : 0.528 8.987 56114 Z= 0.275 Chirality : 0.040 0.275 6769 Planarity : 0.003 0.092 7146 Dihedral : 4.042 24.026 5930 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.80 % Favored : 95.18 % Rotamer: Outliers : 0.03 % Allowed : 0.28 % Favored : 99.69 % 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: 1.00 (0.12), residues: 5543 helix: 1.90 (0.09), residues: 3239 sheet: 0.02 (0.25), residues: 456 loop : -1.47 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 532 HIS 0.003 0.001 HIS G 759 PHE 0.028 0.001 PHE C 107 TYR 0.019 0.001 TYR J 9 ARG 0.006 0.000 ARG C 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 5.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 MET cc_start: 0.2239 (ttt) cc_final: 0.0401 (tpp) REVERT: G 298 MET cc_start: -0.4756 (tmm) cc_final: -0.5730 (ttp) REVERT: G 455 SER cc_start: 0.7279 (m) cc_final: 0.6984 (p) REVERT: G 465 MET cc_start: -0.2954 (tpt) cc_final: -0.3377 (tpp) REVERT: G 602 MET cc_start: -0.1958 (tpt) cc_final: -0.2170 (tpt) REVERT: G 862 MET cc_start: 0.0458 (tpp) cc_final: -0.1157 (ptt) REVERT: G 1148 MET cc_start: 0.2547 (ppp) cc_final: 0.0786 (mmm) REVERT: H 38 MET cc_start: -0.0508 (mtp) cc_final: -0.1491 (mtp) REVERT: H 372 MET cc_start: 0.3532 (pmm) cc_final: 0.2953 (pmm) REVERT: H 479 MET cc_start: -0.0261 (mtm) cc_final: -0.1941 (mtt) REVERT: K 261 MET cc_start: 0.3202 (ttm) cc_final: 0.2333 (ttp) REVERT: L 340 MET cc_start: 0.3508 (mtm) cc_final: 0.3292 (mtm) REVERT: A 301 CYS cc_start: 0.9100 (m) cc_final: 0.8884 (m) REVERT: B 523 MET cc_start: 0.8705 (mtp) cc_final: 0.8244 (mtm) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.5126 time to fit residues: 167.0033 Evaluate side-chains 155 residues out of total 5175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 5.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 349 optimal weight: 5.9990 chunk 469 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 405 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 122 optimal weight: 30.0000 chunk 440 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 452 optimal weight: 0.9980 chunk 55 optimal weight: 40.0000 chunk 81 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN A 615 ASN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.108320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.078694 restraints weight = 425522.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.074754 restraints weight = 320505.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.074785 restraints weight = 259799.566| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.7976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 41068 Z= 0.166 Angle : 0.531 8.838 56114 Z= 0.277 Chirality : 0.040 0.213 6769 Planarity : 0.003 0.060 7146 Dihedral : 3.976 24.253 5930 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.64 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 1.11 (0.12), residues: 5543 helix: 2.01 (0.09), residues: 3243 sheet: 0.11 (0.25), residues: 456 loop : -1.48 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 280 HIS 0.013 0.001 HIS F 186 PHE 0.029 0.001 PHE C 107 TYR 0.020 0.001 TYR A 427 ARG 0.012 0.000 ARG G 443 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6769.04 seconds wall clock time: 130 minutes 38.12 seconds (7838.12 seconds total)