Starting phenix.real_space_refine on Sat Feb 24 06:50:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxl_11524/02_2024/6zxl_11524.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxl_11524/02_2024/6zxl_11524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxl_11524/02_2024/6zxl_11524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxl_11524/02_2024/6zxl_11524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxl_11524/02_2024/6zxl_11524.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxl_11524/02_2024/6zxl_11524.pdb" } resolution = 4.2 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= 0.001 sd= 0.025 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 40 5.16 5 C 26441 2.51 5 N 7348 2.21 5 O 8343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 235": "OD1" <-> "OD2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 441": "OE1" <-> "OE2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 546": "OD1" <-> "OD2" Residue "B TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C ASP 231": "OD1" <-> "OD2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "C ASP 512": "OD1" <-> "OD2" Residue "C PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 535": "OE1" <-> "OE2" Residue "C PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D ASP 497": "OD1" <-> "OD2" Residue "D GLU 502": "OE1" <-> "OE2" Residue "D GLU 525": "OE1" <-> "OE2" Residue "D PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 535": "OE1" <-> "OE2" Residue "D ASP 546": "OD1" <-> "OD2" Residue "D ASP 555": "OD1" <-> "OD2" Residue "D GLU 568": "OE1" <-> "OE2" Residue "D TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 177": "OD1" <-> "OD2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E ASP 231": "OD1" <-> "OD2" Residue "E PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 535": "OE1" <-> "OE2" Residue "E PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 555": "OD1" <-> "OD2" Residue "E ASP 593": "OD1" <-> "OD2" Residue "E TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 195": "OD1" <-> "OD2" Residue "F ASP 235": "OD1" <-> "OD2" Residue "F ASP 265": "OD1" <-> "OD2" Residue "F PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 486": "OE1" <-> "OE2" Residue "F GLU 515": "OE1" <-> "OE2" Residue "F ASP 520": "OD1" <-> "OD2" Residue "F PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 535": "OE1" <-> "OE2" Residue "F ASP 546": "OD1" <-> "OD2" Residue "F PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 235": "OD1" <-> "OD2" Residue "G PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 267": "OE1" <-> "OE2" Residue "G PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 441": "OE1" <-> "OE2" Residue "G ASP 451": "OD1" <-> "OD2" Residue "G GLU 479": "OE1" <-> "OE2" Residue "G PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 535": "OE1" <-> "OE2" Residue "G ASP 546": "OD1" <-> "OD2" Residue "G GLU 609": "OE1" <-> "OE2" Residue "G GLU 618": "OE1" <-> "OE2" Residue "G PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "H ASP 136": "OD1" <-> "OD2" Residue "H GLU 142": "OE1" <-> "OE2" Residue "H PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 257": "OE1" <-> "OE2" Residue "H ASP 415": "OD1" <-> "OD2" Residue "H TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 541": "OE1" <-> "OE2" Residue "H GLU 561": "OE1" <-> "OE2" Residue "H PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 664": "NH1" <-> "NH2" Residue "H TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "I ASP 200": "OD1" <-> "OD2" Residue "I PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 226": "OE1" <-> "OE2" Residue "I ARG 267": "NH1" <-> "NH2" Residue "I ASP 415": "OD1" <-> "OD2" Residue "I PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 497": "OE1" <-> "OE2" Residue "I TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 200": "OD1" <-> "OD2" Residue "J PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 261": "OD1" <-> "OD2" Residue "J TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 415": "OD1" <-> "OD2" Residue "J TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 42172 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3961 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3977 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "C" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3977 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "D" Number of atoms: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3970 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "E" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3977 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "F" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3977 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "G" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3977 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "H" Number of atoms: 5378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5378 Classifications: {'peptide': 699} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 680} Chain breaks: 1 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 4, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 16, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 190 Chain: "I" Number of atoms: 4739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 4739 Classifications: {'peptide': 710} Incomplete info: {'truncation_to_alanine': 310} Link IDs: {'PTRANS': 18, 'TRANS': 691} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1133 Unresolved non-hydrogen angles: 1423 Unresolved non-hydrogen dihedrals: 927 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 9, 'TYR:plan': 10, 'ASN:plan1': 20, 'TRP:plan': 1, 'ASP:plan': 29, 'PHE:plan': 12, 'GLU:plan': 39, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 645 Chain: "J" Number of atoms: 4239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 4239 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 327} Link IDs: {'PTRANS': 16, 'TRANS': 644} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1245 Unresolved non-hydrogen angles: 1551 Unresolved non-hydrogen dihedrals: 1039 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 8, 'TYR:plan': 13, 'ASN:plan1': 23, 'TRP:plan': 2, 'ASP:plan': 27, 'PHE:plan': 14, 'GLU:plan': 41, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 711 Time building chain proxies: 21.30, per 1000 atoms: 0.51 Number of scatterers: 42172 At special positions: 0 Unit cell: (182.97, 179.76, 176.55, 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 40 16.00 O 8343 8.00 N 7348 7.00 C 26441 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: 17.20 Conformation dependent library (CDL) restraints added in 8.4 seconds 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11038 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 82 sheets defined 35.8% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.25 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.522A pdb=" N HIS A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 212' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 234 through 241 removed outlier: 3.669A pdb=" N VAL A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.824A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.862A pdb=" N MET A 350 " --> pdb=" O TRP A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 477 through 487 Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 512 through 517 removed outlier: 4.017A pdb=" N THR A 517 " --> pdb=" O PRO A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.623A pdb=" N PHE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.509A pdb=" N LEU A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 4.561A pdb=" N ASP A 579 " --> pdb=" O THR A 576 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 581 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.578A pdb=" N VAL A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 637 removed outlier: 3.552A pdb=" N LYS A 637 " --> pdb=" O ASP A 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 637' Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.706A pdb=" N ASN A 664 " --> pdb=" O ASP A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 683 removed outlier: 4.097A pdb=" N ASP A 683 " --> pdb=" O LYS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 207 through 213 removed outlier: 3.821A pdb=" N GLU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 removed outlier: 3.707A pdb=" N VAL B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.823A pdb=" N HIS B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 477 through 487 Proline residue: B 482 - end of helix Processing helix chain 'B' and resid 512 through 517 removed outlier: 3.774A pdb=" N THR B 517 " --> pdb=" O PRO B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 532 removed outlier: 3.614A pdb=" N GLY B 532 " --> pdb=" O LYS B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing helix chain 'B' and resid 555 through 568 removed outlier: 3.581A pdb=" N GLU B 568 " --> pdb=" O ASN B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 581 removed outlier: 4.395A pdb=" N ASP B 579 " --> pdb=" O THR B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 removed outlier: 3.590A pdb=" N VAL B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 614 " --> pdb=" O SER B 610 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 615 " --> pdb=" O VAL B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 637 removed outlier: 3.522A pdb=" N LYS B 637 " --> pdb=" O ASP B 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 637' Processing helix chain 'B' and resid 704 through 706 No H-bonds generated for 'chain 'B' and resid 704 through 706' Processing helix chain 'C' and resid 184 through 191 Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.555A pdb=" N HIS C 211 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS C 213 " --> pdb=" O ASN C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 213' Processing helix chain 'C' and resid 234 through 241 removed outlier: 3.739A pdb=" N VAL C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.955A pdb=" N HIS C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 435 through 446 removed outlier: 3.662A pdb=" N PHE C 439 " --> pdb=" O ASN C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Proline residue: C 482 - end of helix Processing helix chain 'C' and resid 512 through 518 Processing helix chain 'C' and resid 522 through 532 removed outlier: 3.580A pdb=" N PHE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 532 " --> pdb=" O LYS C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 568 Processing helix chain 'C' and resid 576 through 581 removed outlier: 4.394A pdb=" N ASP C 579 " --> pdb=" O THR C 576 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 581 " --> pdb=" O LEU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 615 removed outlier: 3.584A pdb=" N VAL C 612 " --> pdb=" O ASP C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 Processing helix chain 'C' and resid 702 through 706 Processing helix chain 'C' and resid 730 through 734 removed outlier: 3.788A pdb=" N ILE C 734 " --> pdb=" O GLY C 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 207 through 213 removed outlier: 3.591A pdb=" N GLU D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 removed outlier: 3.773A pdb=" N VAL D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.882A pdb=" N HIS D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 435 through 446 removed outlier: 3.742A pdb=" N PHE D 439 " --> pdb=" O ASN D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Proline residue: D 482 - end of helix Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 522 through 531 removed outlier: 3.512A pdb=" N PHE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 568 removed outlier: 3.531A pdb=" N GLU D 568 " --> pdb=" O ASN D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 581 removed outlier: 4.271A pdb=" N ASP D 579 " --> pdb=" O THR D 576 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 581 " --> pdb=" O LEU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 615 removed outlier: 3.657A pdb=" N VAL D 612 " --> pdb=" O ASP D 608 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU D 614 " --> pdb=" O SER D 610 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA D 615 " --> pdb=" O VAL D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 638 Processing helix chain 'D' and resid 702 through 706 Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 207 through 213 removed outlier: 3.583A pdb=" N HIS E 211 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 207 through 213' Processing helix chain 'E' and resid 234 through 241 removed outlier: 3.923A pdb=" N VAL E 239 " --> pdb=" O ASP E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.859A pdb=" N HIS E 253 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 477 through 485 Proline residue: E 482 - end of helix Processing helix chain 'E' and resid 512 through 517 removed outlier: 3.915A pdb=" N THR E 517 " --> pdb=" O PRO E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 531 removed outlier: 3.573A pdb=" N PHE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 568 removed outlier: 3.501A pdb=" N GLU E 568 " --> pdb=" O ASN E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 581 removed outlier: 4.467A pdb=" N ASP E 579 " --> pdb=" O THR E 576 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE E 581 " --> pdb=" O LEU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 615 removed outlier: 3.524A pdb=" N VAL E 612 " --> pdb=" O ASP E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 637 removed outlier: 3.613A pdb=" N LYS E 637 " --> pdb=" O ASP E 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 634 through 637' Processing helix chain 'E' and resid 704 through 706 No H-bonds generated for 'chain 'E' and resid 704 through 706' Processing helix chain 'E' and resid 732 through 734 No H-bonds generated for 'chain 'E' and resid 732 through 734' Processing helix chain 'F' and resid 184 through 191 Processing helix chain 'F' and resid 207 through 213 removed outlier: 3.996A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS F 213 " --> pdb=" O ASN F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 241 removed outlier: 3.595A pdb=" N VAL F 239 " --> pdb=" O ASP F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.851A pdb=" N HIS F 253 " --> pdb=" O GLU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 477 through 487 Proline residue: F 482 - end of helix Processing helix chain 'F' and resid 513 through 518 Processing helix chain 'F' and resid 522 through 531 Processing helix chain 'F' and resid 555 through 568 removed outlier: 3.736A pdb=" N GLN F 560 " --> pdb=" O GLN F 556 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN F 561 " --> pdb=" O GLN F 557 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN F 565 " --> pdb=" O ASN F 561 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU F 566 " --> pdb=" O ILE F 562 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA F 567 " --> pdb=" O LYS F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 581 removed outlier: 4.444A pdb=" N ASP F 579 " --> pdb=" O THR F 576 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE F 581 " --> pdb=" O LEU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 615 Processing helix chain 'F' and resid 634 through 637 Processing helix chain 'F' and resid 704 through 706 No H-bonds generated for 'chain 'F' and resid 704 through 706' Processing helix chain 'F' and resid 732 through 734 No H-bonds generated for 'chain 'F' and resid 732 through 734' Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 207 through 212 removed outlier: 4.095A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 234 through 241 removed outlier: 3.659A pdb=" N VAL G 239 " --> pdb=" O ASP G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.915A pdb=" N HIS G 253 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 350 Processing helix chain 'G' and resid 435 through 446 removed outlier: 3.748A pdb=" N PHE G 439 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 487 Proline residue: G 482 - end of helix Processing helix chain 'G' and resid 512 through 517 removed outlier: 3.651A pdb=" N THR G 517 " --> pdb=" O PRO G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 532 removed outlier: 3.761A pdb=" N GLY G 532 " --> pdb=" O LYS G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 555 through 568 Processing helix chain 'G' and resid 576 through 581 removed outlier: 4.567A pdb=" N ASP G 579 " --> pdb=" O THR G 576 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE G 581 " --> pdb=" O LEU G 578 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 615 removed outlier: 3.521A pdb=" N VAL G 612 " --> pdb=" O ASP G 608 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU G 614 " --> pdb=" O SER G 610 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA G 615 " --> pdb=" O VAL G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 637 Processing helix chain 'G' and resid 704 through 706 No H-bonds generated for 'chain 'G' and resid 704 through 706' Processing helix chain 'G' and resid 730 through 734 removed outlier: 3.895A pdb=" N ILE G 734 " --> pdb=" O GLY G 731 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 66 removed outlier: 4.090A pdb=" N VAL H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 99 through 103 Processing helix chain 'H' and resid 140 through 159 removed outlier: 4.496A pdb=" N ASN H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL H 147 " --> pdb=" O LYS H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 164 Processing helix chain 'H' and resid 168 through 179 removed outlier: 4.130A pdb=" N VAL H 173 " --> pdb=" O LYS H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 removed outlier: 4.145A pdb=" N ASP H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU H 188 " --> pdb=" O ASP H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 196 Processing helix chain 'H' and resid 202 through 210 Processing helix chain 'H' and resid 210 through 226 Processing helix chain 'H' and resid 229 through 237 Processing helix chain 'H' and resid 237 through 248 Processing helix chain 'H' and resid 250 through 261 removed outlier: 3.688A pdb=" N LEU H 254 " --> pdb=" O GLN H 250 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU H 257 " --> pdb=" O ASN H 253 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU H 259 " --> pdb=" O SER H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 278 removed outlier: 3.627A pdb=" N GLN H 276 " --> pdb=" O GLU H 272 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N HIS H 277 " --> pdb=" O LYS H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 284 Processing helix chain 'H' and resid 286 through 298 removed outlier: 3.573A pdb=" N ILE H 298 " --> pdb=" O LYS H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 312 removed outlier: 3.573A pdb=" N ILE H 307 " --> pdb=" O LYS H 303 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER H 312 " --> pdb=" O ILE H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 321 removed outlier: 3.873A pdb=" N GLU H 317 " --> pdb=" O GLN H 313 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG H 321 " --> pdb=" O GLU H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 327 removed outlier: 5.649A pdb=" N ASP H 325 " --> pdb=" O ILE H 322 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER H 327 " --> pdb=" O ILE H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 345 removed outlier: 3.610A pdb=" N PHE H 337 " --> pdb=" O GLU H 333 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP H 344 " --> pdb=" O LYS H 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 381 removed outlier: 3.923A pdb=" N PHE H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS H 378 " --> pdb=" O GLU H 374 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU H 381 " --> pdb=" O LYS H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 396 removed outlier: 3.568A pdb=" N GLN H 393 " --> pdb=" O ASN H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 423 Processing helix chain 'H' and resid 442 through 446 Processing helix chain 'H' and resid 447 through 452 Processing helix chain 'H' and resid 464 through 474 removed outlier: 3.766A pdb=" N GLU H 470 " --> pdb=" O GLY H 466 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN H 474 " --> pdb=" O GLU H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 552 through 575 removed outlier: 3.846A pdb=" N LYS H 558 " --> pdb=" O LYS H 554 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS H 572 " --> pdb=" O GLN H 568 " (cutoff:3.500A) Processing helix chain 'H' and resid 591 through 608 removed outlier: 4.122A pdb=" N TYR H 600 " --> pdb=" O VAL H 596 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU H 601 " --> pdb=" O GLU H 597 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASN H 604 " --> pdb=" O TYR H 600 " (cutoff:3.500A) Processing helix chain 'H' and resid 611 through 624 removed outlier: 3.558A pdb=" N ILE H 615 " --> pdb=" O GLN H 611 " (cutoff:3.500A) Processing helix chain 'H' and resid 635 through 639 Processing helix chain 'H' and resid 640 through 647 removed outlier: 3.703A pdb=" N THR H 644 " --> pdb=" O ALA H 640 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS H 645 " --> pdb=" O GLU H 641 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN H 646 " --> pdb=" O GLN H 642 " (cutoff:3.500A) Processing helix chain 'H' and resid 679 through 701 removed outlier: 3.796A pdb=" N GLY H 683 " --> pdb=" O ASN H 679 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY H 697 " --> pdb=" O ASP H 693 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU H 700 " --> pdb=" O ALA H 696 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP H 701 " --> pdb=" O GLY H 697 " (cutoff:3.500A) Processing helix chain 'H' and resid 711 through 721 removed outlier: 4.219A pdb=" N ASP H 716 " --> pdb=" O LYS H 712 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE H 717 " --> pdb=" O LYS H 713 " (cutoff:3.500A) Processing helix chain 'H' and resid 728 through 731 Processing helix chain 'H' and resid 732 through 745 removed outlier: 3.746A pdb=" N ALA H 738 " --> pdb=" O ALA H 734 " (cutoff:3.500A) Processing helix chain 'H' and resid 748 through 759 Processing helix chain 'H' and resid 759 through 772 removed outlier: 3.728A pdb=" N GLN H 764 " --> pdb=" O PRO H 760 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN H 767 " --> pdb=" O PHE H 763 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP H 768 " --> pdb=" O GLN H 764 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN H 769 " --> pdb=" O PHE H 765 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE H 770 " --> pdb=" O ILE H 766 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE H 772 " --> pdb=" O ASP H 768 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 44 removed outlier: 4.324A pdb=" N LYS I 37 " --> pdb=" O GLU I 33 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU I 38 " --> pdb=" O GLU I 34 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE I 39 " --> pdb=" O HIS I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 65 removed outlier: 3.589A pdb=" N LYS I 56 " --> pdb=" O GLU I 52 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS I 65 " --> pdb=" O LYS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 77 removed outlier: 3.956A pdb=" N LEU I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 4.157A pdb=" N ALA I 96 " --> pdb=" O ILE I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 158 removed outlier: 3.765A pdb=" N ASN I 146 " --> pdb=" O GLU I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 163 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.510A pdb=" N LYS I 178 " --> pdb=" O LEU I 174 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN I 179 " --> pdb=" O ASN I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 193 through 197 removed outlier: 3.562A pdb=" N GLU I 196 " --> pdb=" O GLN I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 209 removed outlier: 3.710A pdb=" N LEU I 206 " --> pdb=" O SER I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 226 removed outlier: 3.681A pdb=" N GLN I 214 " --> pdb=" O SER I 210 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU I 215 " --> pdb=" O ASN I 211 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL I 216 " --> pdb=" O GLU I 212 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU I 226 " --> pdb=" O ALA I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 237 removed outlier: 4.287A pdb=" N ASP I 231 " --> pdb=" O PRO I 227 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL I 232 " --> pdb=" O GLN I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 251 Processing helix chain 'I' and resid 252 through 261 Processing helix chain 'I' and resid 263 through 285 removed outlier: 4.046A pdb=" N TYR I 278 " --> pdb=" O ILE I 274 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN I 279 " --> pdb=" O LYS I 275 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N HIS I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TRP I 281 " --> pdb=" O HIS I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 298 removed outlier: 3.711A pdb=" N LEU I 292 " --> pdb=" O GLU I 288 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU I 293 " --> pdb=" O GLY I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 312 removed outlier: 4.037A pdb=" N SER I 312 " --> pdb=" O ILE I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 321 removed outlier: 4.084A pdb=" N GLU I 317 " --> pdb=" O GLN I 313 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG I 321 " --> pdb=" O GLU I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 323 through 327 removed outlier: 3.830A pdb=" N SER I 327 " --> pdb=" O ILE I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 338 Processing helix chain 'I' and resid 372 through 383 removed outlier: 3.903A pdb=" N LEU I 376 " --> pdb=" O GLU I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 396 Processing helix chain 'I' and resid 405 through 421 Processing helix chain 'I' and resid 444 through 446 No H-bonds generated for 'chain 'I' and resid 444 through 446' Processing helix chain 'I' and resid 447 through 452 removed outlier: 3.563A pdb=" N ALA I 452 " --> pdb=" O ALA I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 464 through 473 Processing helix chain 'I' and resid 551 through 574 removed outlier: 3.618A pdb=" N LYS I 558 " --> pdb=" O LYS I 554 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU I 561 " --> pdb=" O THR I 557 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA I 562 " --> pdb=" O LYS I 558 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS I 572 " --> pdb=" O GLN I 568 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU I 574 " --> pdb=" O TRP I 570 " (cutoff:3.500A) Processing helix chain 'I' and resid 591 through 608 removed outlier: 3.802A pdb=" N TYR I 600 " --> pdb=" O VAL I 596 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 624 Processing helix chain 'I' and resid 635 through 639 Processing helix chain 'I' and resid 641 through 646 Processing helix chain 'I' and resid 648 through 652 Processing helix chain 'I' and resid 679 through 699 removed outlier: 3.686A pdb=" N HIS I 690 " --> pdb=" O HIS I 686 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA I 691 " --> pdb=" O GLU I 687 " (cutoff:3.500A) Processing helix chain 'I' and resid 707 through 722 removed outlier: 4.093A pdb=" N LYS I 712 " --> pdb=" O VAL I 708 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS I 713 " --> pdb=" O THR I 709 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP I 716 " --> pdb=" O LYS I 712 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE I 717 " --> pdb=" O LYS I 713 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU I 720 " --> pdb=" O ASP I 716 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU I 721 " --> pdb=" O ILE I 717 " (cutoff:3.500A) Processing helix chain 'I' and resid 723 through 725 No H-bonds generated for 'chain 'I' and resid 723 through 725' Processing helix chain 'I' and resid 732 through 745 Processing helix chain 'I' and resid 748 through 759 Processing helix chain 'I' and resid 759 through 770 removed outlier: 4.065A pdb=" N GLN I 764 " --> pdb=" O PRO I 760 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE I 765 " --> pdb=" O LYS I 761 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 65 removed outlier: 3.525A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 77 removed outlier: 4.184A pdb=" N LEU J 71 " --> pdb=" O PRO J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 96 removed outlier: 4.092A pdb=" N ALA J 96 " --> pdb=" O ILE J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 158 removed outlier: 3.622A pdb=" N ASN J 146 " --> pdb=" O GLU J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 163 Processing helix chain 'J' and resid 167 through 179 removed outlier: 3.525A pdb=" N LYS J 178 " --> pdb=" O LEU J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 193 through 197 Processing helix chain 'J' and resid 202 through 209 removed outlier: 3.630A pdb=" N LEU J 206 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU J 207 " --> pdb=" O VAL J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 226 removed outlier: 3.581A pdb=" N GLU J 226 " --> pdb=" O ALA J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 237 removed outlier: 4.029A pdb=" N ASP J 231 " --> pdb=" O PRO J 227 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL J 232 " --> pdb=" O GLN J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 251 Processing helix chain 'J' and resid 252 through 261 removed outlier: 3.501A pdb=" N LEU J 256 " --> pdb=" O ILE J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 285 removed outlier: 3.685A pdb=" N HIS J 277 " --> pdb=" O LYS J 273 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR J 278 " --> pdb=" O ILE J 274 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N HIS J 280 " --> pdb=" O GLN J 276 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP J 281 " --> pdb=" O HIS J 277 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 298 Processing helix chain 'J' and resid 313 through 320 removed outlier: 3.996A pdb=" N GLU J 317 " --> pdb=" O GLN J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 333 through 338 Processing helix chain 'J' and resid 372 through 383 removed outlier: 3.950A pdb=" N LEU J 376 " --> pdb=" O GLU J 372 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS J 377 " --> pdb=" O LYS J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 388 through 396 Processing helix chain 'J' and resid 406 through 421 removed outlier: 3.665A pdb=" N GLN J 411 " --> pdb=" O ASP J 407 " (cutoff:3.500A) Processing helix chain 'J' and resid 442 through 446 Processing helix chain 'J' and resid 447 through 452 removed outlier: 3.759A pdb=" N ALA J 452 " --> pdb=" O ALA J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 464 through 474 removed outlier: 3.742A pdb=" N GLU J 470 " --> pdb=" O GLY J 466 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASN J 474 " --> pdb=" O GLU J 470 " (cutoff:3.500A) Processing helix chain 'J' and resid 551 through 572 removed outlier: 3.595A pdb=" N LYS J 558 " --> pdb=" O LYS J 554 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU J 561 " --> pdb=" O THR J 557 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS J 572 " --> pdb=" O GLN J 568 " (cutoff:3.500A) Processing helix chain 'J' and resid 591 through 610 removed outlier: 3.732A pdb=" N ILE J 595 " --> pdb=" O TYR J 591 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR J 600 " --> pdb=" O VAL J 596 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU J 601 " --> pdb=" O GLU J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 624 Processing helix chain 'J' and resid 635 through 640 removed outlier: 4.637A pdb=" N ALA J 640 " --> pdb=" O LEU J 636 " (cutoff:3.500A) Processing helix chain 'J' and resid 641 through 646 Processing helix chain 'J' and resid 648 through 652 Processing helix chain 'J' and resid 679 through 700 removed outlier: 4.256A pdb=" N HIS J 690 " --> pdb=" O HIS J 686 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA J 691 " --> pdb=" O GLU J 687 " (cutoff:3.500A) Processing helix chain 'J' and resid 707 through 721 removed outlier: 4.215A pdb=" N LYS J 712 " --> pdb=" O VAL J 708 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS J 713 " --> pdb=" O THR J 709 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP J 716 " --> pdb=" O LYS J 712 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE J 717 " --> pdb=" O LYS J 713 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU J 720 " --> pdb=" O ASP J 716 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU J 721 " --> pdb=" O ILE J 717 " (cutoff:3.500A) Processing helix chain 'J' and resid 722 through 725 removed outlier: 3.687A pdb=" N LEU J 725 " --> pdb=" O GLY J 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 722 through 725' Processing helix chain 'J' and resid 728 through 731 Processing helix chain 'J' and resid 732 through 745 Processing helix chain 'J' and resid 748 through 759 removed outlier: 3.607A pdb=" N VAL J 755 " --> pdb=" O GLU J 751 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN J 756 " --> pdb=" O ARG J 752 " (cutoff:3.500A) Processing helix chain 'J' and resid 759 through 772 removed outlier: 4.100A pdb=" N GLN J 764 " --> pdb=" O PRO J 760 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE J 765 " --> pdb=" O LYS J 761 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE J 770 " --> pdb=" O ILE J 766 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS J 771 " --> pdb=" O ASN J 767 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE J 772 " --> pdb=" O ASP J 768 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 197 removed outlier: 3.597A pdb=" N ASP A 195 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 202 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 394 removed outlier: 7.076A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A 451 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLU A 267 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR A 295 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASP A 265 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N ARG A 297 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N HIS A 263 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE A 269 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN A 361 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU A 271 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG A 359 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 389 through 394 removed outlier: 7.076A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A 451 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLU A 267 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR A 295 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASP A 265 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N ARG A 297 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N HIS A 263 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE A 269 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN A 361 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU A 271 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG A 359 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 364 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 419 " --> pdb=" O ILE A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 458 through 462 removed outlier: 4.245A pdb=" N ILE A 459 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.402A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA7, first strand: chain 'A' and resid 596 through 598 removed outlier: 6.519A pdb=" N HIS A 597 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 628 through 629 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 7.027A pdb=" N VAL A 701 " --> pdb=" O SER A 640 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR A 642 " --> pdb=" O TYR A 699 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR A 699 " --> pdb=" O TYR A 642 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL A 644 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASN A 697 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE A 646 " --> pdb=" O LYS A 695 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LYS A 695 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALA A 700 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU A 725 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 192 through 197 removed outlier: 3.766A pdb=" N ASP B 195 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE B 202 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 389 through 394 removed outlier: 4.943A pdb=" N THR B 390 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 385 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR B 381 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER B 294 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLU B 267 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR B 295 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ASP B 265 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ARG B 297 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N HIS B 263 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 263 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE B 269 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN B 361 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU B 271 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG B 359 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 389 through 394 removed outlier: 4.943A pdb=" N THR B 390 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 385 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR B 381 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER B 294 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLU B 267 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR B 295 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ASP B 265 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ARG B 297 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N HIS B 263 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 263 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE B 269 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN B 361 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU B 271 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG B 359 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 458 through 462 removed outlier: 4.397A pdb=" N ILE B 459 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 501 through 506 Processing sheet with id=AB6, first strand: chain 'B' and resid 541 through 542 Processing sheet with id=AB7, first strand: chain 'B' and resid 596 through 598 Processing sheet with id=AB8, first strand: chain 'B' and resid 628 through 629 Processing sheet with id=AB9, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.860A pdb=" N GLU B 645 " --> pdb=" O ASN B 697 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN B 697 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA B 700 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 725 " --> pdb=" O ALA B 700 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 192 through 197 Processing sheet with id=AC2, first strand: chain 'C' and resid 358 through 360 removed outlier: 7.183A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN C 409 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 389 through 394 removed outlier: 6.777A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU C 448 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLU C 267 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR C 295 " --> pdb=" O ASP C 265 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ASP C 265 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N ARG C 297 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N HIS C 263 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 458 through 462 removed outlier: 5.981A pdb=" N SER C 475 " --> pdb=" O ILE C 459 " (cutoff:3.500A) removed outlier: 10.868A pdb=" N THR C 461 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 9.404A pdb=" N THR C 473 " --> pdb=" O THR C 461 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 501 through 506 removed outlier: 8.587A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG C 592 " --> pdb=" O ASP C 551 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AC7, first strand: chain 'C' and resid 596 through 598 Processing sheet with id=AC8, first strand: chain 'C' and resid 628 through 629 Processing sheet with id=AC9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.687A pdb=" N VAL C 696 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 728 " --> pdb=" O VAL C 696 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL C 698 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA C 700 " --> pdb=" O ILE C 724 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE C 724 " --> pdb=" O ALA C 700 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 192 through 197 removed outlier: 3.632A pdb=" N ASP D 195 " --> pdb=" O PHE D 202 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE D 202 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 262 through 273 removed outlier: 3.956A pdb=" N GLU D 267 " --> pdb=" O ASN D 363 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 262 through 273 removed outlier: 3.956A pdb=" N GLU D 267 " --> pdb=" O ASN D 363 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 293 through 298 removed outlier: 4.269A pdb=" N SER D 329 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR D 381 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU D 385 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR D 390 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 458 through 462 removed outlier: 4.639A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP D 472 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR D 461 " --> pdb=" O ARG D 470 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG D 470 " --> pdb=" O THR D 461 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 501 through 506 removed outlier: 3.549A pdb=" N PHE D 493 " --> pdb=" O VAL D 501 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG D 503 " --> pdb=" O ILE D 491 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE D 491 " --> pdb=" O ARG D 503 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 590 " --> pdb=" O ASN D 553 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AD8, first strand: chain 'D' and resid 596 through 598 Processing sheet with id=AD9, first strand: chain 'D' and resid 628 through 629 Processing sheet with id=AE1, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.217A pdb=" N VAL D 696 " --> pdb=" O SER D 728 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER D 728 " --> pdb=" O VAL D 696 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL D 698 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 724 " --> pdb=" O ALA D 700 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 192 through 197 Processing sheet with id=AE3, first strand: chain 'E' and resid 358 through 360 removed outlier: 3.829A pdb=" N SER E 272 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 389 through 394 removed outlier: 5.251A pdb=" N THR E 390 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU E 385 " --> pdb=" O THR E 390 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA E 392 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR E 381 " --> pdb=" O ILE E 394 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 384 " --> pdb=" O ARG E 449 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG E 449 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLU E 267 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR E 295 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP E 265 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ARG E 297 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N HIS E 263 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE E 364 " --> pdb=" O ILE E 419 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 458 through 462 removed outlier: 5.873A pdb=" N SER E 475 " --> pdb=" O ILE E 459 " (cutoff:3.500A) removed outlier: 10.935A pdb=" N THR E 461 " --> pdb=" O THR E 473 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N THR E 473 " --> pdb=" O THR E 461 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 501 through 506 removed outlier: 3.667A pdb=" N ARG E 592 " --> pdb=" O ASP E 551 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=AE8, first strand: chain 'E' and resid 596 through 598 removed outlier: 6.229A pdb=" N HIS E 597 " --> pdb=" O VAL E 605 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 628 through 629 Processing sheet with id=AF1, first strand: chain 'E' and resid 654 through 655 removed outlier: 3.531A pdb=" N GLY E 641 " --> pdb=" O VAL E 701 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA E 700 " --> pdb=" O LEU E 725 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU E 725 " --> pdb=" O ALA E 700 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 192 through 197 removed outlier: 3.513A pdb=" N ASP F 195 " --> pdb=" O PHE F 202 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE F 202 " --> pdb=" O ASP F 195 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 290 through 292 removed outlier: 6.701A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN F 368 " --> pdb=" O ASN F 409 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN F 409 " --> pdb=" O ASN F 368 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 358 through 360 removed outlier: 6.701A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE F 364 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE F 419 " --> pdb=" O ILE F 364 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 294 through 297 removed outlier: 3.641A pdb=" N SER F 294 " --> pdb=" O ALA F 333 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG F 449 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL F 384 " --> pdb=" O ARG F 449 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 458 through 462 removed outlier: 4.482A pdb=" N ILE F 459 " --> pdb=" O ASP F 472 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR F 461 " --> pdb=" O ARG F 470 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG F 470 " --> pdb=" O THR F 461 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 501 through 506 removed outlier: 3.746A pdb=" N ARG F 592 " --> pdb=" O ASP F 551 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AF9, first strand: chain 'F' and resid 596 through 598 removed outlier: 6.456A pdb=" N HIS F 597 " --> pdb=" O VAL F 605 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 628 through 629 Processing sheet with id=AG2, first strand: chain 'F' and resid 654 through 655 removed outlier: 4.269A pdb=" N GLY F 641 " --> pdb=" O VAL F 701 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL F 696 " --> pdb=" O SER F 728 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER F 728 " --> pdb=" O VAL F 696 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL F 698 " --> pdb=" O ILE F 726 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 724 " --> pdb=" O ALA F 700 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=AG4, first strand: chain 'G' and resid 389 through 394 removed outlier: 4.773A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR G 381 " --> pdb=" O ILE G 394 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER G 382 " --> pdb=" O ASP G 451 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP G 451 " --> pdb=" O SER G 382 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU G 448 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL G 332 " --> pdb=" O LEU G 448 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 450 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN G 328 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU G 267 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR G 295 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASP G 265 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ARG G 297 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N HIS G 263 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE G 269 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ASN G 361 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU G 271 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG G 359 " --> pdb=" O LEU G 271 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN G 368 " --> pdb=" O ASN G 409 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 389 through 394 removed outlier: 4.773A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR G 381 " --> pdb=" O ILE G 394 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER G 382 " --> pdb=" O ASP G 451 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP G 451 " --> pdb=" O SER G 382 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU G 448 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL G 332 " --> pdb=" O LEU G 448 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 450 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN G 328 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU G 267 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR G 295 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASP G 265 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ARG G 297 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N HIS G 263 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE G 269 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ASN G 361 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU G 271 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG G 359 " --> pdb=" O LEU G 271 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 458 through 462 removed outlier: 4.642A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP G 472 " --> pdb=" O ILE G 459 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR G 461 " --> pdb=" O ARG G 470 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG G 470 " --> pdb=" O THR G 461 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.586A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 541 through 542 Processing sheet with id=AG9, first strand: chain 'G' and resid 596 through 598 Processing sheet with id=AH1, first strand: chain 'G' and resid 628 through 629 Processing sheet with id=AH2, first strand: chain 'G' and resid 654 through 655 removed outlier: 3.703A pdb=" N LYS G 695 " --> pdb=" O GLU G 647 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL G 696 " --> pdb=" O SER G 728 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER G 728 " --> pdb=" O VAL G 696 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL G 698 " --> pdb=" O ILE G 726 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 81 through 82 removed outlier: 3.923A pdb=" N TYR H 82 " --> pdb=" O LEU H 129 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 436 through 437 Processing sheet with id=AH5, first strand: chain 'H' and resid 436 through 437 removed outlier: 6.722A pdb=" N LYS H 540 " --> pdb=" O LYS H 536 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LYS H 536 " --> pdb=" O LYS H 540 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TYR H 542 " --> pdb=" O ILE H 534 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE H 534 " --> pdb=" O TYR H 542 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ARG H 544 " --> pdb=" O VAL H 532 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL H 532 " --> pdb=" O ARG H 544 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP H 546 " --> pdb=" O LYS H 530 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS H 530 " --> pdb=" O ASP H 546 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS H 548 " --> pdb=" O GLU H 528 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU H 528 " --> pdb=" O LYS H 548 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 485 through 487 Processing sheet with id=AH7, first strand: chain 'H' and resid 630 through 632 Processing sheet with id=AH8, first strand: chain 'I' and resid 82 through 84 removed outlier: 3.504A pdb=" N TYR I 82 " --> pdb=" O LEU I 129 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE I 131 " --> pdb=" O TYR I 82 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 103 through 105 removed outlier: 3.604A pdb=" N ILE I 104 " --> pdb=" O ALA I 112 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 436 through 442 removed outlier: 3.829A pdb=" N LEU I 437 " --> pdb=" O ILE I 503 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU I 499 " --> pdb=" O MET I 441 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG I 498 " --> pdb=" O ILE I 543 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE I 545 " --> pdb=" O ARG I 498 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LYS I 500 " --> pdb=" O ILE I 545 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ALA I 547 " --> pdb=" O LYS I 500 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ARG I 502 " --> pdb=" O ALA I 547 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL I 549 " --> pdb=" O ARG I 502 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN I 504 " --> pdb=" O VAL I 549 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP I 546 " --> pdb=" O ASP I 531 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP I 531 " --> pdb=" O ASP I 546 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS I 548 " --> pdb=" O ILE I 529 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE I 529 " --> pdb=" O LYS I 548 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL I 550 " --> pdb=" O LEU I 527 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU I 527 " --> pdb=" O VAL I 550 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 455 through 456 removed outlier: 5.818A pdb=" N LYS I 462 " --> pdb=" O ASP I 456 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'I' and resid 485 through 487 Processing sheet with id=AI4, first strand: chain 'I' and resid 583 through 586 removed outlier: 3.535A pdb=" N THR I 584 " --> pdb=" O PHE I 629 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE I 631 " --> pdb=" O THR I 584 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 83 through 84 removed outlier: 4.154A pdb=" N VAL J 128 " --> pdb=" O LYS J 122 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS J 122 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL J 130 " --> pdb=" O TYR J 120 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR J 120 " --> pdb=" O VAL J 130 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 103 through 105 Processing sheet with id=AI7, first strand: chain 'J' and resid 436 through 441 removed outlier: 4.454A pdb=" N LEU J 437 " --> pdb=" O ILE J 503 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE J 503 " --> pdb=" O LEU J 437 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU J 499 " --> pdb=" O MET J 441 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS J 500 " --> pdb=" O ILE J 545 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA J 547 " --> pdb=" O LYS J 500 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ARG J 502 " --> pdb=" O ALA J 547 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL J 549 " --> pdb=" O ARG J 502 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN J 504 " --> pdb=" O VAL J 549 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS J 540 " --> pdb=" O LYS J 536 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS J 536 " --> pdb=" O LYS J 540 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR J 542 " --> pdb=" O ILE J 534 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE J 534 " --> pdb=" O TYR J 542 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ARG J 544 " --> pdb=" O VAL J 532 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL J 532 " --> pdb=" O ARG J 544 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASP J 546 " --> pdb=" O LYS J 530 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 455 through 456 removed outlier: 5.923A pdb=" N LYS J 462 " --> pdb=" O ASP J 456 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'J' and resid 485 through 487 Processing sheet with id=AJ1, first strand: chain 'J' and resid 583 through 586 removed outlier: 3.813A pdb=" N THR J 584 " --> pdb=" O PHE J 629 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE J 631 " --> pdb=" O THR J 584 " (cutoff:3.500A) 1590 hydrogen bonds defined for protein. 4329 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: 19.05 Time building geometry restraints manager: 18.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.47: 24694 1.47 - 1.85: 18171 1.85 - 2.23: 0 2.23 - 2.61: 0 2.61 - 2.98: 2 Bond restraints: 42867 Sorted by residual: bond pdb=" C SER D 301 " pdb=" N GLY D 323 " ideal model delta sigma weight residual 1.331 2.985 -1.654 1.46e-02 4.69e+03 1.28e+04 bond pdb=" C SER G 301 " pdb=" N GLY G 323 " ideal model delta sigma weight residual 1.331 2.984 -1.654 1.46e-02 4.69e+03 1.28e+04 bond pdb=" C THR C 517 " pdb=" N LYS C 518 " ideal model delta sigma weight residual 1.340 1.091 0.249 5.87e-02 2.90e+02 1.80e+01 bond pdb=" C THR G 517 " pdb=" N LYS G 518 " ideal model delta sigma weight residual 1.340 1.096 0.244 5.87e-02 2.90e+02 1.73e+01 bond pdb=" C THR B 517 " pdb=" N LYS B 518 " ideal model delta sigma weight residual 1.340 1.106 0.234 5.87e-02 2.90e+02 1.59e+01 ... (remaining 42862 not shown) Histogram of bond angle deviations from ideal: 72.72 - 86.99: 2 86.99 - 101.27: 60 101.27 - 115.55: 27570 115.55 - 129.83: 30643 129.83 - 144.10: 179 Bond angle restraints: 58454 Sorted by residual: angle pdb=" O SER D 301 " pdb=" C SER D 301 " pdb=" N GLY D 323 " ideal model delta sigma weight residual 121.74 72.72 49.02 1.31e+00 5.83e-01 1.40e+03 angle pdb=" O SER G 301 " pdb=" C SER G 301 " pdb=" N GLY G 323 " ideal model delta sigma weight residual 121.74 81.39 40.35 1.31e+00 5.83e-01 9.49e+02 angle pdb=" C SER D 301 " pdb=" N GLY D 323 " pdb=" CA GLY D 323 " ideal model delta sigma weight residual 121.41 101.61 19.80 1.96e+00 2.60e-01 1.02e+02 angle pdb=" C SER G 301 " pdb=" N GLY G 323 " pdb=" CA GLY G 323 " ideal model delta sigma weight residual 121.41 105.49 15.92 1.96e+00 2.60e-01 6.60e+01 angle pdb=" CA LEU H 582 " pdb=" CB LEU H 582 " pdb=" CG LEU H 582 " ideal model delta sigma weight residual 116.30 139.48 -23.18 3.50e+00 8.16e-02 4.39e+01 ... (remaining 58449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 24201 17.98 - 35.97: 1473 35.97 - 53.95: 175 53.95 - 71.93: 43 71.93 - 89.92: 19 Dihedral angle restraints: 25911 sinusoidal: 8929 harmonic: 16982 Sorted by residual: dihedral pdb=" CA GLN H 165 " pdb=" C GLN H 165 " pdb=" N PRO H 166 " pdb=" CA PRO H 166 " ideal model delta harmonic sigma weight residual 0.00 34.96 -34.96 0 5.00e+00 4.00e-02 4.89e+01 dihedral pdb=" CA LYS D 197 " pdb=" C LYS D 197 " pdb=" N ASN D 198 " pdb=" CA ASN D 198 " ideal model delta harmonic sigma weight residual -180.00 -151.76 -28.24 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA LYS E 197 " pdb=" C LYS E 197 " pdb=" N ASN E 198 " pdb=" CA ASN E 198 " ideal model delta harmonic sigma weight residual 180.00 -152.36 -27.64 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 25908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 6058 0.099 - 0.199: 767 0.199 - 0.298: 68 0.298 - 0.397: 5 0.397 - 0.497: 1 Chirality restraints: 6899 Sorted by residual: chirality pdb=" CB VAL D 175 " pdb=" CA VAL D 175 " pdb=" CG1 VAL D 175 " pdb=" CG2 VAL D 175 " both_signs ideal model delta sigma weight residual False -2.63 -2.13 -0.50 2.00e-01 2.50e+01 6.16e+00 chirality pdb=" CA ARG F 252 " pdb=" N ARG F 252 " pdb=" C ARG F 252 " pdb=" CB ARG F 252 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CB ILE B 432 " pdb=" CA ILE B 432 " pdb=" CG1 ILE B 432 " pdb=" CG2 ILE B 432 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 6896 not shown) Planarity restraints: 7709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 301 " 0.191 2.00e-02 2.50e+03 2.55e-01 6.52e+02 pdb=" C SER D 301 " -0.428 2.00e-02 2.50e+03 pdb=" O SER D 301 " 0.198 2.00e-02 2.50e+03 pdb=" N GLY D 323 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 301 " -0.174 2.00e-02 2.50e+03 2.36e-01 5.59e+02 pdb=" C SER G 301 " 0.399 2.00e-02 2.50e+03 pdb=" O SER G 301 " -0.180 2.00e-02 2.50e+03 pdb=" N GLY G 323 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN I 384 " -0.093 5.00e-02 4.00e+02 1.39e-01 3.09e+01 pdb=" N PRO I 385 " 0.240 5.00e-02 4.00e+02 pdb=" CA PRO I 385 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO I 385 " -0.072 5.00e-02 4.00e+02 ... (remaining 7706 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 482 2.50 - 3.10: 37707 3.10 - 3.70: 64892 3.70 - 4.30: 89173 4.30 - 4.90: 137378 Nonbonded interactions: 329632 Sorted by model distance: nonbonded pdb=" OD1 ASP A 265 " pdb=" OG1 THR A 295 " model vdw 1.897 2.440 nonbonded pdb=" O ILE A 210 " pdb=" NZ LYS A 214 " model vdw 1.946 2.520 nonbonded pdb=" OG SER C 234 " pdb=" OE1 GLU C 237 " model vdw 1.959 2.440 nonbonded pdb=" OG1 THR B 522 " pdb=" OE1 GLU B 525 " model vdw 1.983 2.440 nonbonded pdb=" OG SER C 248 " pdb=" OE1 GLU C 250 " model vdw 2.020 2.440 ... (remaining 329627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 174 through 734) selection = (chain 'B' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) selection = (chain 'C' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) selection = (chain 'D' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) selection = (chain 'E' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) selection = (chain 'F' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) selection = (chain 'G' and (resid 174 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 626 or (resid 627 through 628 \ and (name N or name CA or name C or name O or name CB )) or resid 629 through 67 \ 0 or (resid 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 676 or (resid 677 and (name N or name CA or name C or name O or na \ me CB )) or resid 678 through 734)) } ncs_group { reference = (chain 'H' and ((resid 55 through 56 and (name N or name CA or name C or name O \ or name CB )) or resid 57 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 72 or (resid 73 and (name N or na \ me CA or name C or name O or name CB )) or resid 74 through 79 or (resid 80 and \ (name N or name CA or name C or name O or name CB )) or resid 81 through 86 or ( \ resid 87 through 90 and (name N or name CA or name C or name O or name CB )) or \ resid 91 through 94 or (resid 95 through 96 and (name N or name CA or name C or \ name O or name CB )) or resid 97 or (resid 98 through 103 and (name N or name CA \ or name C or name O or name CB )) or resid 104 or (resid 105 through 106 and (n \ ame N or name CA or name C or name O or name CB )) or resid 107 through 110 or ( \ resid 111 through 113 and (name N or name CA or name C or name O or name CB )) o \ r resid 114 through 119 or (resid 120 through 121 and (name N or name CA or name \ C or name O or name CB )) or resid 122 or (resid 123 and (name N or name CA or \ name C or name O or name CB )) or resid 124 or (resid 125 through 126 and (name \ N or name CA or name C or name O or name CB )) or resid 127 through 161 or (resi \ d 162 and (name N or name CA or name C or name O or name CB )) or resid 163 or ( \ resid 164 through 165 and (name N or name CA or name C or name O or name CB )) o \ r resid 166 through 167 or (resid 168 through 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 192 or (resid 193 and (name N or \ name CA or name C or name O or name CB )) or resid 194 or (resid 195 and (name \ N or name CA or name C or name O or name CB )) or resid 196 through 249 or (resi \ d 250 through 251 and (name N or name CA or name C or name O or name CB )) or re \ sid 252 through 262 or (resid 263 through 270 and (name N or name CA or name C o \ r name O or name CB )) or resid 271 through 272 or (resid 273 through 276 and (n \ ame N or name CA or name C or name O or name CB )) or resid 277 through 279 or ( \ resid 280 and (name N or name CA or name C or name O or name CB )) or resid 281 \ through 283 or (resid 284 through 288 and (name N or name CA or name C or name O \ or name CB )) or resid 289 or (resid 290 and (name N or name CA or name C or na \ me O or name CB )) or (resid 291 through 301 and (name N or name CA or name C or \ name O or name CB )) or (resid 309 through 320 and (name N or name CA or name C \ or name O or name CB )) or (resid 332 through 338 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 369 through 384 and (name N or name CA or \ name C or name O or name CB )) or resid 385 through 387 or (resid 388 through 39 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 392 or (resi \ d 393 through 395 and (name N or name CA or name C or name O or name CB )) or re \ sid 396 through 397 or (resid 405 through 407 and (name N or name CA or name C o \ r name O or name CB )) or resid 408 or (resid 409 through 414 and (name N or nam \ e CA or name C or name O or name CB )) or resid 415 or (resid 416 through 417 an \ d (name N or name CA or name C or name O or name CB )) or resid 418 through 419 \ or (resid 420 through 427 and (name N or name CA or name C or name O or name CB \ )) or resid 428 or (resid 433 through 436 and (name N or name CA or name C or na \ me O or name CB )) or resid 437 through 445 or (resid 446 through 450 and (name \ N or name CA or name C or name O or name CB )) or (resid 451 through 453 and (na \ me N or name CA or name C or name O or name CB )) or resid 454 through 456 or (r \ esid 457 through 459 and (name N or name CA or name C or name O or name CB )) or \ resid 460 through 461 or (resid 462 and (name N or name CA or name C or name O \ or name CB )) or resid 463 or (resid 464 through 465 and (name N or name CA or n \ ame C or name O or name CB )) or resid 466 through 471 or (resid 472 through 473 \ and (name N or name CA or name C or name O or name CB )) or resid 474 or (resid \ 475 through 476 and (name N or name CA or name C or name O or name CB )) or res \ id 477 through 478 or (resid 479 through 480 and (name N or name CA or name C or \ name O or name CB )) or resid 481 through 482 or (resid 483 through 487 and (na \ me N or name CA or name C or name O or name CB )) or resid 488 or (resid 489 thr \ ough 491 and (name N or name CA or name C or name O or name CB )) or resid 492 t \ hrough 494 or (resid 495 through 498 and (name N or name CA or name C or name O \ or name CB )) or resid 499 through 500 or (resid 501 through 502 and (name N or \ name CA or name C or name O or name CB )) or resid 503 through 508 or (resid 509 \ through 511 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 12 through 513 or (resid 514 through 516 and (name N or name CA or name C or nam \ e O or name CB )) or resid 517 or (resid 518 through 525 and (name N or name CA \ or name C or name O or name CB )) or resid 526 or (resid 527 through 533 and (na \ me N or name CA or name C or name O or name CB )) or resid 534 through 536 or (r \ esid 537 and (name N or name CA or name C or name O or name CB )) or resid 538 o \ r (resid 539 through 543 and (name N or name CA or name C or name O or name CB ) \ ) or resid 544 through 547 or (resid 548 and (name N or name CA or name C or nam \ e O or name CB )) or resid 549 or (resid 550 and (name N or name CA or name C or \ name O or name CB )) or resid 551 through 557 or (resid 558 and (name N or name \ CA or name C or name O or name CB )) or resid 559 through 560 or (resid 561 thr \ ough 563 and (name N or name CA or name C or name O or name CB )) or resid 564 o \ r (resid 565 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 66 or (resid 567 through 569 and (name N or name CA or name C or name O or name \ CB )) or resid 570 or (resid 571 through 574 and (name N or name CA or name C or \ name O or name CB )) or resid 575 through 577 or (resid 578 through 579 and (na \ me N or name CA or name C or name O or name CB )) or resid 580 or (resid 581 thr \ ough 582 and (name N or name CA or name C or name O or name CB )) or resid 583 t \ hrough 584 or (resid 585 and (name N or name CA or name C or name O or name CB ) \ ) or resid 586 through 590 or (resid 591 through 592 and (name N or name CA or n \ ame C or name O or name CB )) or resid 593 through 596 or (resid 597 and (name N \ or name CA or name C or name O or name CB )) or resid 598 through 601 or (resid \ 602 through 604 and (name N or name CA or name C or name O or name CB )) or res \ id 605 or (resid 606 through 614 and (name N or name CA or name C or name O or n \ ame CB )) or resid 615 or (resid 616 through 617 and (name N or name CA or name \ C or name O or name CB )) or resid 618 or (resid 619 through 624 and (name N or \ name CA or name C or name O or name CB )) or resid 625 or (resid 626 and (name N \ or name CA or name C or name O or name CB )) or resid 627 or (resid 628 and (na \ me N or name CA or name C or name O or name CB )) or resid 629 through 630 or (r \ esid 631 through 636 and (name N or name CA or name C or name O or name CB )) or \ resid 637 or (resid 638 through 656 and (name N or name CA or name C or name O \ or name CB )) or resid 657 or (resid 658 through 669 and (name N or name CA or n \ ame C or name O or name CB )) or resid 670 or (resid 671 through 673 and (name N \ or name CA or name C or name O or name CB )) or resid 674 or (resid 675 through \ 682 and (name N or name CA or name C or name O or name CB )) or resid 683 or (r \ esid 684 through 688 and (name N or name CA or name C or name O or name CB )) or \ resid 689 or (resid 690 through 696 and (name N or name CA or name C or name O \ or name CB )) or resid 697 or (resid 698 through 710 and (name N or name CA or n \ ame C or name O or name CB )) or resid 711 through 714 or (resid 715 through 721 \ and (name N or name CA or name C or name O or name CB )) or resid 722 or (resid \ 723 through 728 and (name N or name CA or name C or name O or name CB )) or res \ id 729 or (resid 730 through 759 and (name N or name CA or name C or name O or n \ ame CB )) or resid 760 or (resid 761 through 763 and (name N or name CA or name \ C or name O or name CB )) or resid 764 through 765 or (resid 766 through 767 and \ (name N or name CA or name C or name O or name CB )) or resid 768 or (resid 769 \ through 770 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 71 or (resid 772 and (name N or name CA or name C or name O or name CB )) or res \ id 773)) selection = (chain 'I' and ((resid 55 through 56 and (name N or name CA or name C or name O \ or name CB )) or resid 57 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 87 or (resid 88 through 90 and (n \ ame N or name CA or name C or name O or name CB )) or resid 91 through 110 or (r \ esid 111 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 115 or (resid 116 and (name N or name CA or name C or name O \ or name CB )) or resid 117 through 119 or (resid 120 through 121 and (name N or \ name CA or name C or name O or name CB )) or resid 122 through 161 or (resid 162 \ and (name N or name CA or name C or name O or name CB )) or resid 163 through 1 \ 67 or (resid 168 through 169 and (name N or name CA or name C or name O or name \ CB )) or resid 170 through 262 or (resid 263 through 270 and (name N or name CA \ or name C or name O or name CB )) or resid 271 or (resid 272 through 276 and (na \ me N or name CA or name C or name O or name CB )) or resid 277 or (resid 278 thr \ ough 280 and (name N or name CA or name C or name O or name CB )) or resid 281 t \ hrough 282 or (resid 283 through 288 and (name N or name CA or name C or name O \ or name CB )) or (resid 289 through 301 and (name N or name CA or name C or name \ O or name CB )) or resid 309 through 320 or resid 332 through 338 or resid 369 \ through 397 or resid 405 through 412 or (resid 413 through 414 and (name N or na \ me CA or name C or name O or name CB )) or resid 415 through 422 or (resid 423 t \ hrough 427 and (name N or name CA or name C or name O or name CB )) or resid 428 \ or resid 433 through 461 or (resid 462 and (name N or name CA or name C or name \ O or name CB )) or resid 463 or (resid 464 through 465 and (name N or name CA o \ r name C or name O or name CB )) or resid 466 through 471 or (resid 472 through \ 473 and (name N or name CA or name C or name O or name CB )) or resid 474 or (re \ sid 475 through 476 and (name N or name CA or name C or name O or name CB )) or \ resid 477 through 490 or (resid 491 and (name N or name CA or name C or name O o \ r name CB )) or resid 492 through 494 or (resid 495 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 or (resid 500 through 502 \ and (name N or name CA or name C or name O or name CB )) or resid 503 through 51 \ 5 or (resid 516 and (name N or name CA or name C or name O or name CB )) or resi \ d 517 or (resid 518 through 525 and (name N or name CA or name C or name O or na \ me CB )) or (resid 526 through 533 and (name N or name CA or name C or name O or \ name CB )) or resid 534 through 536 or (resid 537 and (name N or name CA or nam \ e C or name O or name CB )) or resid 538 or (resid 539 through 543 and (name N o \ r name CA or name C or name O or name CB )) or resid 544 through 547 or (resid 5 \ 48 and (name N or name CA or name C or name O or name CB )) or resid 549 through \ 562 or (resid 563 and (name N or name CA or name C or name O or name CB )) or r \ esid 564 through 578 or (resid 579 and (name N or name CA or name C or name O or \ name CB )) or resid 580 through 590 or (resid 591 through 592 and (name N or na \ me CA or name C or name O or name CB )) or resid 593 through 596 or (resid 597 a \ nd (name N or name CA or name C or name O or name CB )) or resid 598 through 606 \ or (resid 607 through 614 and (name N or name CA or name C or name O or name CB \ )) or resid 615 through 618 or (resid 619 through 624 and (name N or name CA or \ name C or name O or name CB )) or resid 625 or (resid 626 and (name N or name C \ A or name C or name O or name CB )) or resid 627 through 683 or (resid 684 throu \ gh 688 and (name N or name CA or name C or name O or name CB )) or resid 689 thr \ ough 753 or (resid 754 through 759 and (name N or name CA or name C or name O or \ name CB )) or resid 760 through 768 or (resid 769 through 770 and (name N or na \ me CA or name C or name O or name CB )) or resid 771 or (resid 772 and (name N o \ r name CA or name C or name O or name CB )) or resid 773)) selection = (chain 'J' and (resid 55 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 87 or (resid 88 through 90 and (na \ me N or name CA or name C or name O or name CB )) or resid 91 through 115 or (re \ sid 116 and (name N or name CA or name C or name O or name CB )) or resid 117 th \ rough 124 or (resid 125 through 126 and (name N or name CA or name C or name O o \ r name CB )) or resid 127 through 192 or (resid 193 and (name N or name CA or na \ me C or name O or name CB )) or resid 194 through 249 or (resid 250 through 251 \ and (name N or name CA or name C or name O or name CB )) or resid 252 through 27 \ 3 or (resid 274 through 276 and (name N or name CA or name C or name O or name C \ B )) or resid 277 or (resid 278 through 280 and (name N or name CA or name C or \ name O or name CB )) or resid 281 through 337 or (resid 338 and (name N or name \ CA or name C or name O or name CB )) or resid 369 through 389 or (resid 390 thro \ ugh 391 and (name N or name CA or name C or name O or name CB )) or resid 392 th \ rough 393 or (resid 394 through 395 and (name N or name CA or name C or name O o \ r name CB )) or resid 396 through 397 or (resid 405 through 407 and (name N or n \ ame CA or name C or name O or name CB )) or resid 408 through 410 or (resid 411 \ through 414 and (name N or name CA or name C or name O or name CB )) or resid 41 \ 5 through 423 or (resid 424 through 427 and (name N or name CA or name C or name \ O or name CB )) or resid 428 or (resid 433 through 436 and (name N or name CA o \ r name C or name O or name CB )) or resid 437 through 501 or (resid 502 and (nam \ e N or name CA or name C or name O or name CB )) or resid 503 through 518 or (re \ sid 519 through 525 and (name N or name CA or name C or name O or name CB )) or \ resid 526 through 581 or (resid 582 and (name N or name CA or name C or name O o \ r name CB )) or resid 583 through 663 or (resid 664 through 669 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 670 through 696 and (name N o \ r name CA or name C or name O or name CB )) or resid 697 through 746 or (resid 7 \ 47 through 759 and (name N or name CA or name C or name O or name CB )) or resid \ 760 through 769 or (resid 770 and (name N or name CA or name C or name O or nam \ e CB )) or resid 771 through 773)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.200 Check model and map are aligned: 0.640 Set scattering table: 0.400 Process input model: 111.630 Find NCS groups from input model: 3.590 Set up NCS constraints: 0.190 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 : 0.017 1.654 42867 Z= 1.229 Angle : 1.383 49.025 58454 Z= 0.762 Chirality : 0.066 0.497 6899 Planarity : 0.009 0.255 7709 Dihedral : 11.909 89.916 14873 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 32.99 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.03 % Favored : 91.62 % Rotamer: Outliers : 0.10 % Allowed : 0.52 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -2.81 (0.10), residues: 5704 helix: -1.84 (0.12), residues: 1499 sheet: -0.98 (0.16), residues: 901 loop : -2.19 (0.09), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.005 TRP I 501 HIS 0.032 0.004 HIS D 299 PHE 0.070 0.005 PHE B 531 TYR 0.069 0.004 TYR I 167 ARG 0.017 0.001 ARG D 297 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11408 Ramachandran restraints generated. 5704 Oldfield, 0 Emsley, 5704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 954 time to evaluate : 4.988 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.9031 (p0) cc_final: 0.8784 (p0) REVERT: A 225 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8466 (ttpt) REVERT: A 247 VAL cc_start: 0.9558 (t) cc_final: 0.9193 (p) REVERT: A 368 ASN cc_start: 0.8560 (t0) cc_final: 0.8359 (t0) REVERT: A 383 LEU cc_start: 0.8667 (tp) cc_final: 0.8231 (tt) REVERT: A 391 LEU cc_start: 0.9383 (mm) cc_final: 0.9130 (mm) REVERT: A 415 ASN cc_start: 0.8766 (m110) cc_final: 0.8436 (m110) REVERT: A 450 LEU cc_start: 0.8791 (mt) cc_final: 0.8046 (mp) REVERT: A 462 TYR cc_start: 0.8031 (t80) cc_final: 0.7721 (t80) REVERT: A 465 GLU cc_start: 0.8582 (mp0) cc_final: 0.8129 (pp20) REVERT: A 512 ASP cc_start: 0.8314 (t0) cc_final: 0.8069 (t0) REVERT: A 583 LEU cc_start: 0.9524 (mt) cc_final: 0.9104 (mt) REVERT: A 584 ASN cc_start: 0.9055 (m110) cc_final: 0.8656 (t0) REVERT: A 727 PHE cc_start: 0.8783 (t80) cc_final: 0.8393 (t80) REVERT: B 192 TYR cc_start: 0.9165 (p90) cc_final: 0.8093 (p90) REVERT: B 262 VAL cc_start: 0.9462 (t) cc_final: 0.9115 (p) REVERT: B 293 THR cc_start: 0.8054 (p) cc_final: 0.7454 (p) REVERT: B 328 ASN cc_start: 0.8161 (t0) cc_final: 0.7673 (t0) REVERT: B 368 ASN cc_start: 0.9049 (t0) cc_final: 0.8844 (t0) REVERT: B 404 ILE cc_start: 0.9313 (mm) cc_final: 0.8811 (mp) REVERT: B 437 ASN cc_start: 0.9265 (m110) cc_final: 0.8799 (t0) REVERT: B 439 PHE cc_start: 0.9431 (t80) cc_final: 0.9139 (t80) REVERT: B 486 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8474 (tm-30) REVERT: B 524 LYS cc_start: 0.9282 (tmtt) cc_final: 0.8938 (tptp) REVERT: B 561 ASN cc_start: 0.8965 (m110) cc_final: 0.8600 (m110) REVERT: B 581 ILE cc_start: 0.9211 (mt) cc_final: 0.8976 (mm) REVERT: B 590 LEU cc_start: 0.9128 (tp) cc_final: 0.8909 (tp) REVERT: B 616 HIS cc_start: 0.9177 (m90) cc_final: 0.8889 (m90) REVERT: B 705 ASN cc_start: 0.9170 (m-40) cc_final: 0.8639 (p0) REVERT: B 726 ILE cc_start: 0.8739 (mm) cc_final: 0.8526 (mm) REVERT: B 727 PHE cc_start: 0.8112 (t80) cc_final: 0.7525 (t80) REVERT: C 326 ASN cc_start: 0.8025 (p0) cc_final: 0.7622 (p0) REVERT: C 343 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7539 (mp0) REVERT: C 408 ASN cc_start: 0.9277 (t0) cc_final: 0.9026 (t0) REVERT: C 434 MET cc_start: 0.8812 (ppp) cc_final: 0.8516 (ppp) REVERT: C 437 ASN cc_start: 0.9324 (m110) cc_final: 0.8790 (t0) REVERT: C 439 PHE cc_start: 0.9426 (t80) cc_final: 0.9189 (t80) REVERT: C 528 LYS cc_start: 0.9227 (ttmm) cc_final: 0.8772 (mmtt) REVERT: C 552 PHE cc_start: 0.9129 (m-80) cc_final: 0.8852 (m-10) REVERT: C 583 LEU cc_start: 0.9471 (mm) cc_final: 0.9151 (mm) REVERT: C 727 PHE cc_start: 0.7601 (t80) cc_final: 0.7265 (t80) REVERT: D 292 ASN cc_start: 0.8976 (m110) cc_final: 0.8466 (t0) REVERT: D 365 ARG cc_start: 0.7221 (ttm-80) cc_final: 0.6866 (tpp-160) REVERT: D 394 ILE cc_start: 0.9309 (mm) cc_final: 0.9080 (mp) REVERT: D 439 PHE cc_start: 0.9458 (t80) cc_final: 0.9256 (t80) REVERT: D 454 GLN cc_start: 0.8743 (mp10) cc_final: 0.8514 (mp10) REVERT: D 462 TYR cc_start: 0.8457 (t80) cc_final: 0.8043 (t80) REVERT: D 486 GLU cc_start: 0.8026 (tt0) cc_final: 0.7796 (tt0) REVERT: D 501 VAL cc_start: 0.9468 (t) cc_final: 0.9221 (p) REVERT: D 525 GLU cc_start: 0.8838 (tp30) cc_final: 0.8186 (tp30) REVERT: D 565 GLN cc_start: 0.9460 (mm-40) cc_final: 0.9250 (mm110) REVERT: E 192 TYR cc_start: 0.9192 (p90) cc_final: 0.8848 (p90) REVERT: E 195 ASP cc_start: 0.7899 (p0) cc_final: 0.7515 (p0) REVERT: E 203 LEU cc_start: 0.8314 (tp) cc_final: 0.8020 (tp) REVERT: E 242 ARG cc_start: 0.8946 (mpp-170) cc_final: 0.8574 (mtm-85) REVERT: E 247 VAL cc_start: 0.9445 (t) cc_final: 0.9200 (p) REVERT: E 436 TYR cc_start: 0.8957 (t80) cc_final: 0.8602 (t80) REVERT: E 472 ASP cc_start: 0.8954 (t0) cc_final: 0.8586 (t0) REVERT: E 486 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8294 (tp30) REVERT: E 509 ASN cc_start: 0.8904 (t0) cc_final: 0.8676 (t0) REVERT: E 512 ASP cc_start: 0.8544 (t0) cc_final: 0.8338 (t0) REVERT: E 553 ASN cc_start: 0.8985 (m110) cc_final: 0.8664 (m-40) REVERT: E 583 LEU cc_start: 0.9109 (mt) cc_final: 0.8802 (mt) REVERT: E 616 HIS cc_start: 0.9126 (m90) cc_final: 0.8744 (p-80) REVERT: E 704 GLU cc_start: 0.9056 (pt0) cc_final: 0.8762 (pt0) REVERT: F 190 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8359 (tm-30) REVERT: F 195 ASP cc_start: 0.8715 (t0) cc_final: 0.8449 (t0) REVERT: F 226 TRP cc_start: 0.8967 (t60) cc_final: 0.8524 (t-100) REVERT: F 326 ASN cc_start: 0.7827 (m-40) cc_final: 0.7338 (m-40) REVERT: F 366 TYR cc_start: 0.8847 (m-10) cc_final: 0.8561 (m-10) REVERT: F 454 GLN cc_start: 0.8481 (mp10) cc_final: 0.8268 (mp10) REVERT: F 472 ASP cc_start: 0.9404 (t0) cc_final: 0.9154 (t0) REVERT: F 501 VAL cc_start: 0.9134 (t) cc_final: 0.8777 (p) REVERT: F 512 ASP cc_start: 0.7670 (m-30) cc_final: 0.7453 (m-30) REVERT: F 520 ASP cc_start: 0.7674 (t0) cc_final: 0.7380 (t0) REVERT: F 529 ILE cc_start: 0.9217 (mm) cc_final: 0.8914 (tp) REVERT: F 551 ASP cc_start: 0.7325 (t0) cc_final: 0.7039 (t0) REVERT: F 590 LEU cc_start: 0.8484 (mp) cc_final: 0.8063 (pp) REVERT: F 708 ILE cc_start: 0.9059 (pt) cc_final: 0.8774 (tp) REVERT: F 732 TYR cc_start: 0.8680 (p90) cc_final: 0.8208 (p90) REVERT: G 192 TYR cc_start: 0.8541 (p90) cc_final: 0.7796 (p90) REVERT: G 211 HIS cc_start: 0.9185 (m90) cc_final: 0.8847 (m90) REVERT: G 224 GLU cc_start: 0.8649 (tp30) cc_final: 0.7957 (tp30) REVERT: G 515 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8344 (tm-30) REVERT: G 516 THR cc_start: 0.8910 (m) cc_final: 0.8342 (p) REVERT: G 518 LYS cc_start: 0.9452 (pttt) cc_final: 0.9102 (pttp) REVERT: G 551 ASP cc_start: 0.8721 (t0) cc_final: 0.7246 (p0) REVERT: G 561 ASN cc_start: 0.9460 (t0) cc_final: 0.9116 (t0) REVERT: G 565 GLN cc_start: 0.8966 (mt0) cc_final: 0.8607 (mm-40) REVERT: G 629 LEU cc_start: 0.8968 (mm) cc_final: 0.8763 (mm) REVERT: H 74 TYR cc_start: 0.8294 (t80) cc_final: 0.8035 (t80) REVERT: H 120 TYR cc_start: 0.8399 (t80) cc_final: 0.8150 (t80) REVERT: H 201 PHE cc_start: 0.8716 (m-80) cc_final: 0.8177 (m-80) REVERT: H 232 VAL cc_start: 0.9295 (t) cc_final: 0.9046 (t) REVERT: H 236 TYR cc_start: 0.8249 (m-80) cc_final: 0.7919 (m-10) REVERT: H 244 MET cc_start: 0.9214 (tpt) cc_final: 0.8596 (tpp) REVERT: H 391 ARG cc_start: 0.9095 (ppt170) cc_final: 0.8608 (tmm-80) REVERT: H 441 MET cc_start: 0.8615 (tmm) cc_final: 0.8186 (tmm) REVERT: H 484 MET cc_start: 0.8102 (mpp) cc_final: 0.7627 (mpp) REVERT: H 486 VAL cc_start: 0.9100 (m) cc_final: 0.8830 (p) REVERT: H 499 LEU cc_start: 0.8857 (mp) cc_final: 0.8142 (mp) REVERT: H 521 LEU cc_start: 0.9631 (mm) cc_final: 0.9287 (mm) REVERT: H 584 THR cc_start: 0.8132 (t) cc_final: 0.7396 (p) REVERT: H 611 GLN cc_start: 0.7989 (tp-100) cc_final: 0.7785 (tp40) REVERT: H 628 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.7690 (mtm-85) REVERT: H 631 PHE cc_start: 0.9399 (m-80) cc_final: 0.9006 (m-80) REVERT: H 693 ASP cc_start: 0.9025 (t70) cc_final: 0.8772 (t0) REVERT: H 736 PHE cc_start: 0.8544 (t80) cc_final: 0.8074 (t80) REVERT: H 737 PHE cc_start: 0.8984 (m-80) cc_final: 0.8387 (m-80) REVERT: H 741 PHE cc_start: 0.9653 (t80) cc_final: 0.9292 (t80) REVERT: H 745 HIS cc_start: 0.9053 (m90) cc_final: 0.8574 (m90) REVERT: I 35 HIS cc_start: 0.7970 (m90) cc_final: 0.7726 (m90) REVERT: I 150 GLU cc_start: 0.9574 (mm-30) cc_final: 0.9372 (mm-30) REVERT: I 158 ASP cc_start: 0.8897 (m-30) cc_final: 0.8548 (m-30) REVERT: I 182 ASP cc_start: 0.8871 (t0) cc_final: 0.8524 (p0) REVERT: I 205 PHE cc_start: 0.8439 (m-80) cc_final: 0.8167 (m-80) REVERT: I 215 GLU cc_start: 0.8683 (mp0) cc_final: 0.8377 (pm20) REVERT: I 247 PHE cc_start: 0.9637 (t80) cc_final: 0.9345 (t80) REVERT: J 217 PHE cc_start: 0.9203 (t80) cc_final: 0.8741 (t80) REVERT: J 221 PHE cc_start: 0.8963 (t80) cc_final: 0.8220 (t80) REVERT: J 277 HIS cc_start: 0.9149 (t-90) cc_final: 0.8923 (t-90) REVERT: J 436 TYR cc_start: 0.6982 (m-10) cc_final: 0.6509 (m-80) REVERT: J 544 ARG cc_start: 0.4630 (mmp80) cc_final: 0.4344 (mmp80) outliers start: 4 outliers final: 2 residues processed: 956 average time/residue: 0.5508 time to fit residues: 849.0659 Evaluate side-chains 784 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 782 time to evaluate : 5.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 481 optimal weight: 6.9990 chunk 432 optimal weight: 3.9990 chunk 239 optimal weight: 0.3980 chunk 147 optimal weight: 0.7980 chunk 291 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 446 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 271 optimal weight: 6.9990 chunk 332 optimal weight: 2.9990 chunk 517 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 GLN B 588 ASN B 602 ASN C 573 ASN C 602 ASN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN E 483 GLN E 541 GLN E 560 GLN E 602 ASN F 458 ASN ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 GLN G 602 ASN ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 516 ASN ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 594 ASN ** H 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 690 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 469 ASN ** I 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 HIS J 228 GLN J 405 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 42867 Z= 0.244 Angle : 0.695 13.032 58454 Z= 0.366 Chirality : 0.047 0.237 6899 Planarity : 0.005 0.076 7709 Dihedral : 4.979 31.353 6111 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.22 % Favored : 95.71 % Rotamer: Outliers : 0.30 % Allowed : 4.73 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.47 (0.11), residues: 5708 helix: -0.56 (0.12), residues: 1644 sheet: -0.77 (0.15), residues: 1022 loop : -1.25 (0.11), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP I 501 HIS 0.016 0.001 HIS C 616 PHE 0.026 0.002 PHE I 765 TYR 0.024 0.002 TYR D 542 ARG 0.008 0.001 ARG A 449 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1044 time to evaluate : 5.004 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8778 (p0) cc_final: 0.8429 (p0) REVERT: A 192 TYR cc_start: 0.9000 (p90) cc_final: 0.8314 (p90) REVERT: A 200 ARG cc_start: 0.7890 (mpt180) cc_final: 0.7562 (mpt-90) REVERT: A 222 SER cc_start: 0.9265 (t) cc_final: 0.8908 (p) REVERT: A 225 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8376 (ttpt) REVERT: A 247 VAL cc_start: 0.9493 (t) cc_final: 0.9094 (p) REVERT: A 250 GLU cc_start: 0.8874 (mp0) cc_final: 0.8576 (tp30) REVERT: A 324 PHE cc_start: 0.8343 (p90) cc_final: 0.7997 (p90) REVERT: A 391 LEU cc_start: 0.9228 (mm) cc_final: 0.8980 (mm) REVERT: A 436 TYR cc_start: 0.9162 (t80) cc_final: 0.8833 (t80) REVERT: A 462 TYR cc_start: 0.8004 (t80) cc_final: 0.7779 (t80) REVERT: A 465 GLU cc_start: 0.8636 (mp0) cc_final: 0.8402 (mp0) REVERT: A 485 GLN cc_start: 0.8962 (pm20) cc_final: 0.8662 (pm20) REVERT: A 492 ILE cc_start: 0.9494 (mm) cc_final: 0.9190 (tp) REVERT: A 515 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8508 (mm-30) REVERT: A 566 LEU cc_start: 0.9595 (pp) cc_final: 0.9279 (tp) REVERT: A 568 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8823 (pm20) REVERT: A 584 ASN cc_start: 0.9082 (m110) cc_final: 0.8705 (t0) REVERT: A 633 LYS cc_start: 0.9410 (tmmt) cc_final: 0.9009 (tptp) REVERT: A 727 PHE cc_start: 0.8853 (t80) cc_final: 0.8507 (t80) REVERT: B 192 TYR cc_start: 0.9326 (p90) cc_final: 0.8097 (p90) REVERT: B 219 TYR cc_start: 0.8712 (m-10) cc_final: 0.8233 (m-10) REVERT: B 220 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8561 (mmmm) REVERT: B 244 ASP cc_start: 0.8580 (t70) cc_final: 0.7921 (t0) REVERT: B 246 ASN cc_start: 0.9118 (m110) cc_final: 0.8552 (m110) REVERT: B 368 ASN cc_start: 0.9243 (t0) cc_final: 0.8950 (t0) REVERT: B 378 LEU cc_start: 0.9109 (tp) cc_final: 0.8373 (tt) REVERT: B 439 PHE cc_start: 0.9318 (t80) cc_final: 0.9074 (t80) REVERT: B 509 ASN cc_start: 0.8660 (t0) cc_final: 0.8389 (t0) REVERT: B 515 GLU cc_start: 0.8600 (tp30) cc_final: 0.8298 (tp30) REVERT: B 525 GLU cc_start: 0.9033 (mp0) cc_final: 0.8824 (mp0) REVERT: B 550 PHE cc_start: 0.8919 (m-80) cc_final: 0.8211 (m-80) REVERT: B 555 ASP cc_start: 0.9213 (t0) cc_final: 0.8950 (t70) REVERT: B 561 ASN cc_start: 0.8951 (m110) cc_final: 0.8601 (m-40) REVERT: B 581 ILE cc_start: 0.8964 (mt) cc_final: 0.8685 (mm) REVERT: B 705 ASN cc_start: 0.9070 (m-40) cc_final: 0.8694 (p0) REVERT: B 721 ILE cc_start: 0.8418 (mm) cc_final: 0.8149 (mm) REVERT: B 727 PHE cc_start: 0.8295 (t80) cc_final: 0.7870 (t80) REVERT: C 231 ASP cc_start: 0.8933 (p0) cc_final: 0.8728 (p0) REVERT: C 234 SER cc_start: 0.7029 (p) cc_final: 0.6056 (p) REVERT: C 243 ILE cc_start: 0.9364 (tp) cc_final: 0.8734 (pt) REVERT: C 326 ASN cc_start: 0.8089 (p0) cc_final: 0.7525 (p0) REVERT: C 375 TYR cc_start: 0.8301 (m-80) cc_final: 0.7993 (m-10) REVERT: C 381 THR cc_start: 0.8848 (t) cc_final: 0.8558 (m) REVERT: C 434 MET cc_start: 0.9145 (ppp) cc_final: 0.8902 (ppp) REVERT: C 439 PHE cc_start: 0.9421 (t80) cc_final: 0.9086 (t80) REVERT: C 462 TYR cc_start: 0.9099 (t80) cc_final: 0.8842 (t80) REVERT: C 486 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8546 (tm-30) REVERT: C 487 THR cc_start: 0.9044 (p) cc_final: 0.8810 (p) REVERT: C 552 PHE cc_start: 0.8903 (m-80) cc_final: 0.8447 (m-10) REVERT: C 590 LEU cc_start: 0.9391 (tt) cc_final: 0.9088 (tt) REVERT: C 596 PHE cc_start: 0.8985 (m-80) cc_final: 0.8581 (m-10) REVERT: C 636 ARG cc_start: 0.8655 (ptt-90) cc_final: 0.8305 (ptp90) REVERT: C 727 PHE cc_start: 0.7864 (t80) cc_final: 0.7378 (t80) REVERT: D 190 GLU cc_start: 0.8738 (tp30) cc_final: 0.8343 (tp30) REVERT: D 195 ASP cc_start: 0.8090 (t0) cc_final: 0.7762 (t0) REVERT: D 365 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7333 (tpp-160) REVERT: D 408 ASN cc_start: 0.9094 (t0) cc_final: 0.8884 (t0) REVERT: D 447 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7630 (tm-30) REVERT: D 462 TYR cc_start: 0.8388 (t80) cc_final: 0.8020 (t80) REVERT: D 501 VAL cc_start: 0.9168 (t) cc_final: 0.8955 (p) REVERT: D 542 TYR cc_start: 0.9159 (t80) cc_final: 0.8906 (t80) REVERT: D 565 GLN cc_start: 0.9426 (mm-40) cc_final: 0.9028 (mt0) REVERT: E 216 LEU cc_start: 0.9087 (mt) cc_final: 0.8801 (mt) REVERT: E 240 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8387 (t) REVERT: E 509 ASN cc_start: 0.8982 (t0) cc_final: 0.8750 (t0) REVERT: E 512 ASP cc_start: 0.7893 (t0) cc_final: 0.6963 (t0) REVERT: E 525 GLU cc_start: 0.8775 (pt0) cc_final: 0.8196 (pt0) REVERT: E 553 ASN cc_start: 0.8406 (m110) cc_final: 0.8041 (m-40) REVERT: E 575 TYR cc_start: 0.8286 (m-80) cc_final: 0.7253 (m-80) REVERT: F 190 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8294 (tm-30) REVERT: F 223 PRO cc_start: 0.9389 (Cg_endo) cc_final: 0.9136 (Cg_exo) REVERT: F 226 TRP cc_start: 0.9007 (t60) cc_final: 0.8636 (t60) REVERT: F 261 ILE cc_start: 0.9635 (mm) cc_final: 0.9421 (tp) REVERT: F 265 ASP cc_start: 0.8833 (t0) cc_final: 0.8539 (p0) REVERT: F 326 ASN cc_start: 0.7813 (m-40) cc_final: 0.7177 (m-40) REVERT: F 332 VAL cc_start: 0.7976 (p) cc_final: 0.7679 (p) REVERT: F 419 ILE cc_start: 0.9224 (tp) cc_final: 0.9024 (tp) REVERT: F 439 PHE cc_start: 0.9539 (t80) cc_final: 0.9306 (t80) REVERT: F 442 LEU cc_start: 0.9768 (tt) cc_final: 0.9530 (pp) REVERT: F 459 ILE cc_start: 0.8977 (mt) cc_final: 0.8769 (tp) REVERT: F 462 TYR cc_start: 0.7572 (t80) cc_final: 0.7192 (t80) REVERT: F 471 VAL cc_start: 0.8303 (m) cc_final: 0.7519 (t) REVERT: F 501 VAL cc_start: 0.9135 (t) cc_final: 0.8841 (p) REVERT: F 523 LEU cc_start: 0.9282 (tt) cc_final: 0.9056 (tt) REVERT: F 542 TYR cc_start: 0.9062 (t80) cc_final: 0.8793 (t80) REVERT: F 551 ASP cc_start: 0.7211 (t0) cc_final: 0.6293 (p0) REVERT: F 602 ASN cc_start: 0.9393 (m-40) cc_final: 0.9072 (m-40) REVERT: F 708 ILE cc_start: 0.9062 (pt) cc_final: 0.8764 (tp) REVERT: F 732 TYR cc_start: 0.8653 (p90) cc_final: 0.8200 (p90) REVERT: G 440 LEU cc_start: 0.9200 (mt) cc_final: 0.8897 (mt) REVERT: G 453 ASP cc_start: 0.9170 (p0) cc_final: 0.8841 (p0) REVERT: G 492 ILE cc_start: 0.9679 (mm) cc_final: 0.9428 (tp) REVERT: G 500 LEU cc_start: 0.8599 (mt) cc_final: 0.8081 (mt) REVERT: G 512 ASP cc_start: 0.8306 (t0) cc_final: 0.6654 (t0) REVERT: G 515 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8369 (mm-30) REVERT: G 551 ASP cc_start: 0.8817 (t0) cc_final: 0.7808 (p0) REVERT: G 569 LEU cc_start: 0.9195 (mt) cc_final: 0.8890 (mp) REVERT: G 582 LYS cc_start: 0.9382 (mmtm) cc_final: 0.9153 (mmmt) REVERT: G 602 ASN cc_start: 0.8470 (m-40) cc_final: 0.8121 (m110) REVERT: G 629 LEU cc_start: 0.8787 (mm) cc_final: 0.8459 (mm) REVERT: G 638 ILE cc_start: 0.9054 (pt) cc_final: 0.8221 (mm) REVERT: H 62 LEU cc_start: 0.9497 (mp) cc_final: 0.9194 (mt) REVERT: H 120 TYR cc_start: 0.8380 (t80) cc_final: 0.8039 (t80) REVERT: H 170 PHE cc_start: 0.9266 (t80) cc_final: 0.8754 (t80) REVERT: H 174 LEU cc_start: 0.9594 (mt) cc_final: 0.9350 (mt) REVERT: H 200 ASP cc_start: 0.9381 (p0) cc_final: 0.9135 (p0) REVERT: H 201 PHE cc_start: 0.8590 (m-80) cc_final: 0.8247 (m-80) REVERT: H 217 PHE cc_start: 0.8828 (t80) cc_final: 0.8435 (t80) REVERT: H 234 GLN cc_start: 0.8904 (mt0) cc_final: 0.8553 (mt0) REVERT: H 281 TRP cc_start: 0.8462 (t60) cc_final: 0.8021 (t60) REVERT: H 391 ARG cc_start: 0.9229 (ppt170) cc_final: 0.8928 (ptm-80) REVERT: H 438 TYR cc_start: 0.8319 (m-80) cc_final: 0.7901 (m-80) REVERT: H 441 MET cc_start: 0.8163 (tmm) cc_final: 0.7929 (tmm) REVERT: H 484 MET cc_start: 0.8126 (mpp) cc_final: 0.7610 (mpp) REVERT: H 486 VAL cc_start: 0.8851 (m) cc_final: 0.8610 (p) REVERT: H 499 LEU cc_start: 0.8639 (mp) cc_final: 0.7790 (mp) REVERT: H 521 LEU cc_start: 0.9475 (mm) cc_final: 0.9077 (mm) REVERT: H 545 ILE cc_start: 0.9067 (mm) cc_final: 0.8641 (pt) REVERT: H 582 LEU cc_start: 0.8774 (pp) cc_final: 0.8426 (mm) REVERT: H 591 TYR cc_start: 0.8704 (t80) cc_final: 0.7954 (t80) REVERT: H 628 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.7882 (mtm-85) REVERT: H 684 PHE cc_start: 0.9067 (t80) cc_final: 0.8722 (t80) REVERT: H 736 PHE cc_start: 0.8692 (t80) cc_final: 0.8245 (t80) REVERT: H 737 PHE cc_start: 0.9054 (m-80) cc_final: 0.8482 (m-80) REVERT: I 35 HIS cc_start: 0.7989 (m90) cc_final: 0.7672 (m-70) REVERT: I 81 ILE cc_start: 0.9097 (pt) cc_final: 0.8607 (pt) REVERT: I 108 TYR cc_start: 0.8441 (m-10) cc_final: 0.8149 (m-10) REVERT: I 149 TYR cc_start: 0.8987 (t80) cc_final: 0.8567 (t80) REVERT: I 157 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7986 (ttp80) REVERT: I 182 ASP cc_start: 0.8726 (t0) cc_final: 0.8493 (p0) REVERT: I 205 PHE cc_start: 0.8331 (m-80) cc_final: 0.8071 (m-80) REVERT: I 215 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8468 (pp20) REVERT: I 230 ARG cc_start: 0.8596 (ttm-80) cc_final: 0.7755 (tpp80) REVERT: I 267 ARG cc_start: 0.9138 (ptp90) cc_final: 0.8777 (ptt-90) REVERT: I 268 TYR cc_start: 0.8905 (t80) cc_final: 0.8567 (t80) REVERT: I 544 ARG cc_start: 0.6946 (tpt90) cc_final: 0.6576 (tpt170) REVERT: I 545 ILE cc_start: 0.8714 (mp) cc_final: 0.8448 (mp) REVERT: I 597 GLU cc_start: 0.6847 (mp0) cc_final: 0.6432 (mp0) REVERT: J 115 HIS cc_start: 0.8600 (p-80) cc_final: 0.8014 (p-80) REVERT: J 117 HIS cc_start: 0.7209 (t-90) cc_final: 0.6557 (t70) REVERT: J 217 PHE cc_start: 0.9177 (t80) cc_final: 0.8642 (t80) REVERT: J 221 PHE cc_start: 0.8991 (t80) cc_final: 0.8293 (t80) REVERT: J 223 TYR cc_start: 0.8484 (m-80) cc_final: 0.8167 (m-80) REVERT: J 244 MET cc_start: 0.9374 (tpt) cc_final: 0.9140 (tpp) REVERT: J 277 HIS cc_start: 0.9130 (t-90) cc_final: 0.8915 (t-90) REVERT: J 436 TYR cc_start: 0.6852 (m-10) cc_final: 0.6388 (m-80) REVERT: J 590 ARG cc_start: 0.7453 (tpm170) cc_final: 0.7154 (ttp-110) outliers start: 12 outliers final: 2 residues processed: 1054 average time/residue: 0.5454 time to fit residues: 939.4958 Evaluate side-chains 848 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 843 time to evaluate : 4.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 287 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 430 optimal weight: 20.0000 chunk 352 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 518 optimal weight: 8.9990 chunk 560 optimal weight: 30.0000 chunk 461 optimal weight: 10.0000 chunk 514 optimal weight: 8.9990 chunk 176 optimal weight: 0.9990 chunk 416 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 GLN B 616 HIS C 246 ASN C 602 ASN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN E 483 GLN E 541 GLN E 553 ASN F 328 ASN F 388 ASN F 458 ASN ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 HIS H 168 GLN H 277 HIS ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 594 ASN ** H 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 690 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 GLN ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.135 42867 Z= 0.424 Angle : 0.741 11.990 58454 Z= 0.388 Chirality : 0.046 0.215 6899 Planarity : 0.005 0.071 7709 Dihedral : 5.099 26.341 6111 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.94 % Favored : 94.01 % Rotamer: Outliers : 0.07 % Allowed : 5.50 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -1.18 (0.11), residues: 5708 helix: -0.38 (0.13), residues: 1658 sheet: -0.63 (0.15), residues: 1113 loop : -1.01 (0.11), residues: 2937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 570 HIS 0.008 0.002 HIS B 253 PHE 0.035 0.002 PHE B 550 TYR 0.027 0.002 TYR G 411 ARG 0.011 0.001 ARG E 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 908 time to evaluate : 4.748 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8731 (p0) cc_final: 0.8409 (p0) REVERT: A 190 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8266 (tm-30) REVERT: A 192 TYR cc_start: 0.9117 (p90) cc_final: 0.8495 (p90) REVERT: A 200 ARG cc_start: 0.7802 (mpt180) cc_final: 0.7357 (mpt-90) REVERT: A 225 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8511 (ttpt) REVERT: A 324 PHE cc_start: 0.8462 (p90) cc_final: 0.8058 (p90) REVERT: A 391 LEU cc_start: 0.9267 (mm) cc_final: 0.8972 (mm) REVERT: A 415 ASN cc_start: 0.8759 (m110) cc_final: 0.8444 (m110) REVERT: A 436 TYR cc_start: 0.9194 (t80) cc_final: 0.8908 (t80) REVERT: A 453 ASP cc_start: 0.8758 (p0) cc_final: 0.7970 (p0) REVERT: A 465 GLU cc_start: 0.8662 (mp0) cc_final: 0.8425 (mp0) REVERT: A 492 ILE cc_start: 0.9634 (mm) cc_final: 0.9412 (tp) REVERT: A 525 GLU cc_start: 0.9342 (mp0) cc_final: 0.9059 (mp0) REVERT: A 547 ILE cc_start: 0.9400 (tp) cc_final: 0.9184 (mm) REVERT: A 552 PHE cc_start: 0.9249 (m-80) cc_final: 0.8944 (m-80) REVERT: A 583 LEU cc_start: 0.9473 (mt) cc_final: 0.8955 (mt) REVERT: A 584 ASN cc_start: 0.9111 (m110) cc_final: 0.8700 (m110) REVERT: A 727 PHE cc_start: 0.8980 (t80) cc_final: 0.8493 (t80) REVERT: B 185 ASP cc_start: 0.8747 (p0) cc_final: 0.8521 (p0) REVERT: B 192 TYR cc_start: 0.9235 (p90) cc_final: 0.8125 (p90) REVERT: B 225 LYS cc_start: 0.9056 (tttm) cc_final: 0.8785 (ttpt) REVERT: B 236 PHE cc_start: 0.9133 (t80) cc_final: 0.8678 (t80) REVERT: B 244 ASP cc_start: 0.8730 (t70) cc_final: 0.8519 (t0) REVERT: B 246 ASN cc_start: 0.9179 (m110) cc_final: 0.8893 (m110) REVERT: B 439 PHE cc_start: 0.9346 (t80) cc_final: 0.9134 (t80) REVERT: B 504 ARG cc_start: 0.7683 (mtp180) cc_final: 0.7253 (mtp180) REVERT: B 512 ASP cc_start: 0.8213 (t0) cc_final: 0.7989 (t0) REVERT: B 515 GLU cc_start: 0.8570 (tp30) cc_final: 0.8060 (tp30) REVERT: B 561 ASN cc_start: 0.8981 (m110) cc_final: 0.8589 (m110) REVERT: B 579 ASP cc_start: 0.9000 (p0) cc_final: 0.8780 (p0) REVERT: B 584 ASN cc_start: 0.8438 (t0) cc_final: 0.8159 (t0) REVERT: B 705 ASN cc_start: 0.9147 (m-40) cc_final: 0.8658 (p0) REVERT: B 727 PHE cc_start: 0.8459 (t80) cc_final: 0.8030 (t80) REVERT: C 225 LYS cc_start: 0.9140 (tptm) cc_final: 0.8917 (tttm) REVERT: C 243 ILE cc_start: 0.9437 (tp) cc_final: 0.9146 (tp) REVERT: C 326 ASN cc_start: 0.8155 (p0) cc_final: 0.7534 (p0) REVERT: C 336 HIS cc_start: 0.9120 (p-80) cc_final: 0.8765 (p-80) REVERT: C 343 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7490 (mp0) REVERT: C 368 ASN cc_start: 0.8379 (t0) cc_final: 0.8115 (t0) REVERT: C 486 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8550 (tm-30) REVERT: C 497 ASP cc_start: 0.8081 (p0) cc_final: 0.7827 (p0) REVERT: C 528 LYS cc_start: 0.9140 (ttmm) cc_final: 0.8598 (mmtt) REVERT: C 551 ASP cc_start: 0.8820 (t0) cc_final: 0.8598 (t70) REVERT: C 552 PHE cc_start: 0.8819 (m-80) cc_final: 0.8618 (m-80) REVERT: C 555 ASP cc_start: 0.8804 (t0) cc_final: 0.8587 (t0) REVERT: C 590 LEU cc_start: 0.9370 (tt) cc_final: 0.9044 (tt) REVERT: C 596 PHE cc_start: 0.9201 (m-80) cc_final: 0.8971 (m-80) REVERT: C 636 ARG cc_start: 0.8645 (ptt-90) cc_final: 0.8346 (ptp90) REVERT: C 727 PHE cc_start: 0.7786 (t80) cc_final: 0.7283 (t80) REVERT: D 190 GLU cc_start: 0.8850 (tp30) cc_final: 0.8513 (tp30) REVERT: D 192 TYR cc_start: 0.9246 (p90) cc_final: 0.8772 (p90) REVERT: D 195 ASP cc_start: 0.8135 (t0) cc_final: 0.7864 (t0) REVERT: D 297 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7817 (ttp80) REVERT: D 365 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7343 (tpp-160) REVERT: D 394 ILE cc_start: 0.9203 (mp) cc_final: 0.8984 (mp) REVERT: D 408 ASN cc_start: 0.9161 (t0) cc_final: 0.8891 (t0) REVERT: D 411 TYR cc_start: 0.8426 (t80) cc_final: 0.8174 (t80) REVERT: D 439 PHE cc_start: 0.9480 (t80) cc_final: 0.9268 (t80) REVERT: D 486 GLU cc_start: 0.8736 (tt0) cc_final: 0.8484 (tt0) REVERT: D 525 GLU cc_start: 0.8794 (mp0) cc_final: 0.8522 (mp0) REVERT: D 533 PHE cc_start: 0.8816 (m-10) cc_final: 0.8431 (m-10) REVERT: D 565 GLN cc_start: 0.9478 (mm-40) cc_final: 0.9037 (mt0) REVERT: D 638 ILE cc_start: 0.8887 (pt) cc_final: 0.8446 (pt) REVERT: D 703 LYS cc_start: 0.9515 (mppt) cc_final: 0.9195 (mmtm) REVERT: E 224 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8353 (mm-30) REVERT: E 436 TYR cc_start: 0.8791 (t80) cc_final: 0.8303 (t80) REVERT: E 439 PHE cc_start: 0.9440 (t80) cc_final: 0.9151 (t80) REVERT: E 509 ASN cc_start: 0.9262 (t0) cc_final: 0.8897 (t0) REVERT: E 512 ASP cc_start: 0.8182 (t0) cc_final: 0.6520 (t0) REVERT: E 553 ASN cc_start: 0.8843 (m-40) cc_final: 0.8333 (m-40) REVERT: E 575 TYR cc_start: 0.8270 (m-80) cc_final: 0.7361 (m-80) REVERT: E 580 LYS cc_start: 0.9600 (mmmt) cc_final: 0.9397 (mmmt) REVERT: F 176 PRO cc_start: 0.8399 (Cg_exo) cc_final: 0.8078 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8320 (tm-30) REVERT: F 195 ASP cc_start: 0.8905 (t0) cc_final: 0.8631 (t0) REVERT: F 223 PRO cc_start: 0.9379 (Cg_endo) cc_final: 0.9020 (Cg_exo) REVERT: F 226 TRP cc_start: 0.9298 (t60) cc_final: 0.9029 (t60) REVERT: F 265 ASP cc_start: 0.8807 (t0) cc_final: 0.8591 (p0) REVERT: F 326 ASN cc_start: 0.7750 (m-40) cc_final: 0.7161 (m-40) REVERT: F 332 VAL cc_start: 0.8203 (p) cc_final: 0.7915 (p) REVERT: F 366 TYR cc_start: 0.8924 (m-10) cc_final: 0.8695 (m-10) REVERT: F 439 PHE cc_start: 0.9556 (t80) cc_final: 0.9308 (t80) REVERT: F 462 TYR cc_start: 0.7803 (t80) cc_final: 0.7442 (t80) REVERT: F 471 VAL cc_start: 0.8390 (m) cc_final: 0.7842 (t) REVERT: F 497 ASP cc_start: 0.8684 (p0) cc_final: 0.8417 (p0) REVERT: F 501 VAL cc_start: 0.9247 (t) cc_final: 0.8960 (p) REVERT: F 512 ASP cc_start: 0.8096 (m-30) cc_final: 0.7776 (m-30) REVERT: F 525 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8964 (pt0) REVERT: F 551 ASP cc_start: 0.7538 (t0) cc_final: 0.6749 (p0) REVERT: F 633 LYS cc_start: 0.9157 (pptt) cc_final: 0.8927 (pptt) REVERT: F 708 ILE cc_start: 0.9123 (pt) cc_final: 0.8876 (tp) REVERT: G 211 HIS cc_start: 0.9168 (m90) cc_final: 0.8773 (m170) REVERT: G 328 ASN cc_start: 0.7760 (t0) cc_final: 0.7542 (t0) REVERT: G 453 ASP cc_start: 0.8904 (p0) cc_final: 0.8590 (p0) REVERT: G 492 ILE cc_start: 0.9575 (mm) cc_final: 0.9297 (tp) REVERT: G 512 ASP cc_start: 0.8292 (t0) cc_final: 0.6696 (t0) REVERT: G 515 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8502 (mm-30) REVERT: G 525 GLU cc_start: 0.8888 (pp20) cc_final: 0.8675 (pp20) REVERT: G 551 ASP cc_start: 0.8899 (t0) cc_final: 0.7871 (p0) REVERT: G 552 PHE cc_start: 0.8960 (m-80) cc_final: 0.8671 (m-80) REVERT: G 561 ASN cc_start: 0.9526 (t0) cc_final: 0.9321 (t0) REVERT: G 582 LYS cc_start: 0.9406 (mmtm) cc_final: 0.9168 (mmmt) REVERT: G 602 ASN cc_start: 0.8401 (m-40) cc_final: 0.8079 (m110) REVERT: G 727 PHE cc_start: 0.8137 (t80) cc_final: 0.7655 (t80) REVERT: H 74 TYR cc_start: 0.7956 (t80) cc_final: 0.7609 (t80) REVERT: H 120 TYR cc_start: 0.8408 (t80) cc_final: 0.8024 (t80) REVERT: H 170 PHE cc_start: 0.9356 (t80) cc_final: 0.8797 (t80) REVERT: H 174 LEU cc_start: 0.9639 (mt) cc_final: 0.9338 (mt) REVERT: H 200 ASP cc_start: 0.9351 (p0) cc_final: 0.9117 (p0) REVERT: H 217 PHE cc_start: 0.8884 (t80) cc_final: 0.8480 (t80) REVERT: H 234 GLN cc_start: 0.8926 (mt0) cc_final: 0.8318 (mp10) REVERT: H 259 LEU cc_start: 0.9498 (mm) cc_final: 0.9297 (mm) REVERT: H 281 TRP cc_start: 0.8599 (t60) cc_final: 0.8192 (t60) REVERT: H 391 ARG cc_start: 0.9220 (ppt170) cc_final: 0.8964 (ttp80) REVERT: H 438 TYR cc_start: 0.8352 (m-80) cc_final: 0.8002 (m-80) REVERT: H 441 MET cc_start: 0.8249 (tmm) cc_final: 0.7819 (tmm) REVERT: H 470 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8315 (mp0) REVERT: H 484 MET cc_start: 0.8149 (mpp) cc_final: 0.7584 (mpp) REVERT: H 486 VAL cc_start: 0.8875 (m) cc_final: 0.8627 (p) REVERT: H 499 LEU cc_start: 0.8645 (mp) cc_final: 0.7320 (mp) REVERT: H 521 LEU cc_start: 0.9526 (mm) cc_final: 0.9068 (mm) REVERT: H 591 TYR cc_start: 0.8686 (t80) cc_final: 0.7793 (t80) REVERT: H 595 ILE cc_start: 0.9471 (mm) cc_final: 0.9217 (mm) REVERT: H 611 GLN cc_start: 0.8290 (tp40) cc_final: 0.8049 (tp40) REVERT: H 684 PHE cc_start: 0.9019 (t80) cc_final: 0.8740 (t80) REVERT: H 736 PHE cc_start: 0.8774 (t80) cc_final: 0.8359 (t80) REVERT: H 737 PHE cc_start: 0.9095 (m-80) cc_final: 0.8529 (m-80) REVERT: I 35 HIS cc_start: 0.7989 (m90) cc_final: 0.7751 (m-70) REVERT: I 108 TYR cc_start: 0.8399 (m-10) cc_final: 0.8119 (m-10) REVERT: I 139 GLU cc_start: 0.7895 (tt0) cc_final: 0.7611 (tt0) REVERT: I 149 TYR cc_start: 0.9190 (t80) cc_final: 0.8965 (t80) REVERT: I 157 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8087 (ttp80) REVERT: I 158 ASP cc_start: 0.9009 (m-30) cc_final: 0.8598 (m-30) REVERT: I 189 LEU cc_start: 0.8743 (mt) cc_final: 0.8537 (mt) REVERT: I 205 PHE cc_start: 0.8343 (m-80) cc_final: 0.8085 (m-10) REVERT: I 230 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8245 (ttm110) REVERT: I 259 LEU cc_start: 0.9091 (pp) cc_final: 0.8697 (mt) REVERT: I 264 MET cc_start: 0.8792 (pmm) cc_final: 0.8503 (pmm) REVERT: I 267 ARG cc_start: 0.9064 (ptp90) cc_final: 0.8703 (ptt-90) REVERT: I 268 TYR cc_start: 0.8862 (t80) cc_final: 0.8410 (t80) REVERT: I 281 TRP cc_start: 0.8718 (t60) cc_final: 0.8425 (t60) REVERT: I 441 MET cc_start: 0.6521 (tmm) cc_final: 0.5315 (tmm) REVERT: I 544 ARG cc_start: 0.6948 (tpt90) cc_final: 0.6610 (tpt90) REVERT: I 545 ILE cc_start: 0.8719 (mp) cc_final: 0.8518 (mp) REVERT: I 597 GLU cc_start: 0.6899 (mp0) cc_final: 0.6523 (mp0) REVERT: J 217 PHE cc_start: 0.9153 (t80) cc_final: 0.8652 (t80) REVERT: J 221 PHE cc_start: 0.8924 (t80) cc_final: 0.8385 (t80) REVERT: J 223 TYR cc_start: 0.8599 (m-80) cc_final: 0.8261 (m-80) REVERT: J 243 TYR cc_start: 0.8612 (t80) cc_final: 0.8030 (t80) REVERT: J 247 PHE cc_start: 0.9073 (m-80) cc_final: 0.8516 (m-80) REVERT: J 277 HIS cc_start: 0.9077 (t-90) cc_final: 0.8869 (t-90) REVERT: J 436 TYR cc_start: 0.6917 (m-10) cc_final: 0.6536 (m-80) outliers start: 3 outliers final: 0 residues processed: 911 average time/residue: 0.5456 time to fit residues: 804.6679 Evaluate side-chains 777 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 777 time to evaluate : 4.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 512 optimal weight: 6.9990 chunk 389 optimal weight: 5.9990 chunk 269 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 348 optimal weight: 4.9990 chunk 520 optimal weight: 4.9990 chunk 550 optimal weight: 0.9980 chunk 271 optimal weight: 3.9990 chunk 493 optimal weight: 10.0000 chunk 148 optimal weight: 50.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A 616 HIS ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 GLN B 697 ASN C 422 ASN C 602 ASN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN E 483 GLN ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 594 ASN ** H 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 638 ASN ** H 690 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 769 GLN J 117 HIS ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 42867 Z= 0.349 Angle : 0.665 11.662 58454 Z= 0.350 Chirality : 0.046 0.199 6899 Planarity : 0.005 0.080 7709 Dihedral : 5.020 24.145 6111 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.66 % Favored : 94.32 % Rotamer: Outliers : 0.07 % Allowed : 4.78 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.99 (0.11), residues: 5708 helix: -0.19 (0.13), residues: 1655 sheet: -0.49 (0.15), residues: 1085 loop : -0.92 (0.11), residues: 2968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 570 HIS 0.006 0.001 HIS E 336 PHE 0.022 0.002 PHE B 531 TYR 0.028 0.002 TYR G 411 ARG 0.010 0.001 ARG H 391 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 935 time to evaluate : 5.321 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: 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: symmetry clash REVERT: A 185 ASP cc_start: 0.8798 (p0) cc_final: 0.8464 (p0) REVERT: A 190 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8257 (tm-30) REVERT: A 192 TYR cc_start: 0.9078 (p90) cc_final: 0.8515 (p90) REVERT: A 200 ARG cc_start: 0.7665 (mpt180) cc_final: 0.7160 (mpt-90) REVERT: A 225 LYS cc_start: 0.8896 (ttmt) cc_final: 0.8677 (ttpt) REVERT: A 243 ILE cc_start: 0.9340 (tt) cc_final: 0.9111 (tt) REVERT: A 324 PHE cc_start: 0.8474 (p90) cc_final: 0.8008 (p90) REVERT: A 391 LEU cc_start: 0.9249 (mm) cc_final: 0.8986 (mm) REVERT: A 415 ASN cc_start: 0.8775 (m110) cc_final: 0.8459 (m110) REVERT: A 436 TYR cc_start: 0.9139 (t80) cc_final: 0.8566 (t80) REVERT: A 453 ASP cc_start: 0.8874 (p0) cc_final: 0.8260 (p0) REVERT: A 465 GLU cc_start: 0.8694 (mp0) cc_final: 0.8401 (mp0) REVERT: A 485 GLN cc_start: 0.8838 (pm20) cc_final: 0.8584 (pm20) REVERT: A 490 ARG cc_start: 0.8754 (ptm160) cc_final: 0.8224 (ptm-80) REVERT: A 515 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8573 (mm-30) REVERT: A 525 GLU cc_start: 0.9337 (mp0) cc_final: 0.9080 (mp0) REVERT: A 547 ILE cc_start: 0.9399 (tp) cc_final: 0.9191 (mm) REVERT: A 552 PHE cc_start: 0.9238 (m-80) cc_final: 0.8970 (m-80) REVERT: A 602 ASN cc_start: 0.9056 (m-40) cc_final: 0.8799 (m-40) REVERT: A 727 PHE cc_start: 0.9027 (t80) cc_final: 0.8546 (t80) REVERT: B 185 ASP cc_start: 0.8720 (p0) cc_final: 0.8378 (p0) REVERT: B 190 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8223 (tm-30) REVERT: B 192 TYR cc_start: 0.9166 (p90) cc_final: 0.8328 (p90) REVERT: B 227 SER cc_start: 0.9190 (p) cc_final: 0.8885 (m) REVERT: B 236 PHE cc_start: 0.9088 (t80) cc_final: 0.8781 (t80) REVERT: B 244 ASP cc_start: 0.8626 (t70) cc_final: 0.8426 (t0) REVERT: B 246 ASN cc_start: 0.9164 (m110) cc_final: 0.8894 (m110) REVERT: B 328 ASN cc_start: 0.7743 (t0) cc_final: 0.7246 (t0) REVERT: B 378 LEU cc_start: 0.9216 (tp) cc_final: 0.8556 (tt) REVERT: B 470 ARG cc_start: 0.8302 (ptp90) cc_final: 0.7577 (ttp80) REVERT: B 504 ARG cc_start: 0.7769 (mtp180) cc_final: 0.6753 (mtp-110) REVERT: B 512 ASP cc_start: 0.8374 (t0) cc_final: 0.8139 (t0) REVERT: B 515 GLU cc_start: 0.8544 (tp30) cc_final: 0.7745 (tm-30) REVERT: B 561 ASN cc_start: 0.8986 (m110) cc_final: 0.8616 (m110) REVERT: B 705 ASN cc_start: 0.9174 (m-40) cc_final: 0.8627 (p0) REVERT: B 727 PHE cc_start: 0.8526 (t80) cc_final: 0.8145 (t80) REVERT: C 195 ASP cc_start: 0.8173 (t0) cc_final: 0.7818 (t0) REVERT: C 326 ASN cc_start: 0.8267 (p0) cc_final: 0.7712 (p0) REVERT: C 336 HIS cc_start: 0.9137 (p-80) cc_final: 0.8640 (p-80) REVERT: C 368 ASN cc_start: 0.8479 (t0) cc_final: 0.8256 (t0) REVERT: C 434 MET cc_start: 0.8872 (ppp) cc_final: 0.8571 (ppp) REVERT: C 486 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8549 (tm-30) REVERT: C 497 ASP cc_start: 0.8166 (p0) cc_final: 0.7832 (p0) REVERT: C 525 GLU cc_start: 0.9022 (pp20) cc_final: 0.8801 (pp20) REVERT: C 551 ASP cc_start: 0.8835 (t0) cc_final: 0.8630 (t70) REVERT: C 552 PHE cc_start: 0.8712 (m-80) cc_final: 0.8248 (m-80) REVERT: C 575 TYR cc_start: 0.7194 (m-80) cc_final: 0.6737 (m-80) REVERT: C 590 LEU cc_start: 0.9326 (tt) cc_final: 0.9020 (tt) REVERT: C 596 PHE cc_start: 0.9038 (m-80) cc_final: 0.8097 (m-80) REVERT: C 727 PHE cc_start: 0.7862 (t80) cc_final: 0.7369 (t80) REVERT: D 195 ASP cc_start: 0.8265 (t0) cc_final: 0.7991 (t0) REVERT: D 263 HIS cc_start: 0.8127 (p90) cc_final: 0.7914 (p-80) REVERT: D 299 HIS cc_start: 0.8894 (t-90) cc_final: 0.8502 (t-90) REVERT: D 365 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7338 (tpp-160) REVERT: D 367 VAL cc_start: 0.9427 (t) cc_final: 0.9080 (m) REVERT: D 408 ASN cc_start: 0.9186 (t0) cc_final: 0.8881 (t0) REVERT: D 439 PHE cc_start: 0.9478 (t80) cc_final: 0.9273 (t80) REVERT: D 447 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7707 (tm-30) REVERT: D 525 GLU cc_start: 0.8771 (mp0) cc_final: 0.8460 (mp0) REVERT: D 565 GLN cc_start: 0.9458 (mm-40) cc_final: 0.9056 (mt0) REVERT: D 617 ARG cc_start: 0.8966 (ptp-110) cc_final: 0.8692 (ptp-110) REVERT: D 635 ILE cc_start: 0.9367 (tt) cc_final: 0.9033 (pt) REVERT: D 638 ILE cc_start: 0.8893 (pt) cc_final: 0.8373 (pt) REVERT: D 703 LYS cc_start: 0.9494 (mppt) cc_final: 0.9148 (mmtm) REVERT: E 225 LYS cc_start: 0.9120 (mmmt) cc_final: 0.8913 (mtpp) REVERT: E 240 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8414 (t) REVERT: E 436 TYR cc_start: 0.8700 (t80) cc_final: 0.8317 (t80) REVERT: E 509 ASN cc_start: 0.9267 (t0) cc_final: 0.8921 (t0) REVERT: E 512 ASP cc_start: 0.8135 (t0) cc_final: 0.7815 (t0) REVERT: E 553 ASN cc_start: 0.8851 (m-40) cc_final: 0.8477 (m-40) REVERT: E 575 TYR cc_start: 0.8294 (m-80) cc_final: 0.7357 (m-80) REVERT: F 176 PRO cc_start: 0.8492 (Cg_exo) cc_final: 0.8220 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8310 (tm-30) REVERT: F 223 PRO cc_start: 0.9399 (Cg_endo) cc_final: 0.9010 (Cg_exo) REVERT: F 226 TRP cc_start: 0.9380 (t60) cc_final: 0.9036 (t60) REVERT: F 265 ASP cc_start: 0.8832 (t0) cc_final: 0.8473 (p0) REVERT: F 326 ASN cc_start: 0.7744 (m-40) cc_final: 0.7123 (m-40) REVERT: F 366 TYR cc_start: 0.8912 (m-10) cc_final: 0.8634 (m-10) REVERT: F 439 PHE cc_start: 0.9544 (t80) cc_final: 0.9243 (t80) REVERT: F 453 ASP cc_start: 0.8877 (p0) cc_final: 0.8595 (p0) REVERT: F 454 GLN cc_start: 0.8007 (mp10) cc_final: 0.7797 (mp10) REVERT: F 462 TYR cc_start: 0.7816 (t80) cc_final: 0.7425 (t80) REVERT: F 471 VAL cc_start: 0.8287 (m) cc_final: 0.7624 (t) REVERT: F 501 VAL cc_start: 0.9269 (t) cc_final: 0.9010 (p) REVERT: F 512 ASP cc_start: 0.7969 (m-30) cc_final: 0.7678 (m-30) REVERT: F 521 MET cc_start: 0.8204 (pmm) cc_final: 0.7965 (pmm) REVERT: F 542 TYR cc_start: 0.9119 (t80) cc_final: 0.8896 (t80) REVERT: F 551 ASP cc_start: 0.7608 (t0) cc_final: 0.6824 (p0) REVERT: F 708 ILE cc_start: 0.9099 (pt) cc_final: 0.8851 (tp) REVERT: G 365 ARG cc_start: 0.7595 (mtt-85) cc_final: 0.7228 (mtt-85) REVERT: G 439 PHE cc_start: 0.9260 (t80) cc_final: 0.9051 (t80) REVERT: G 448 LEU cc_start: 0.9365 (mm) cc_final: 0.9140 (mm) REVERT: G 453 ASP cc_start: 0.8923 (p0) cc_final: 0.8712 (p0) REVERT: G 492 ILE cc_start: 0.9585 (mm) cc_final: 0.9350 (tp) REVERT: G 512 ASP cc_start: 0.8331 (t0) cc_final: 0.7926 (t0) REVERT: G 521 MET cc_start: 0.7005 (pmm) cc_final: 0.6698 (pmm) REVERT: G 551 ASP cc_start: 0.8929 (t0) cc_final: 0.7905 (p0) REVERT: G 552 PHE cc_start: 0.8978 (m-80) cc_final: 0.8646 (m-80) REVERT: G 560 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8377 (mp10) REVERT: G 561 ASN cc_start: 0.9514 (t0) cc_final: 0.9248 (t0) REVERT: G 582 LYS cc_start: 0.9411 (mmtm) cc_final: 0.9177 (mmmt) REVERT: G 602 ASN cc_start: 0.8327 (m-40) cc_final: 0.8019 (m110) REVERT: G 638 ILE cc_start: 0.9074 (pt) cc_final: 0.8294 (mm) REVERT: G 727 PHE cc_start: 0.8134 (t80) cc_final: 0.7661 (t80) REVERT: H 74 TYR cc_start: 0.7774 (t80) cc_final: 0.7487 (t80) REVERT: H 120 TYR cc_start: 0.8409 (t80) cc_final: 0.8179 (t80) REVERT: H 145 LEU cc_start: 0.9122 (mt) cc_final: 0.8872 (mt) REVERT: H 170 PHE cc_start: 0.9317 (t80) cc_final: 0.8733 (t80) REVERT: H 174 LEU cc_start: 0.9661 (mt) cc_final: 0.9426 (mt) REVERT: H 200 ASP cc_start: 0.9410 (p0) cc_final: 0.9174 (p0) REVERT: H 217 PHE cc_start: 0.8812 (t80) cc_final: 0.8414 (t80) REVERT: H 234 GLN cc_start: 0.8969 (mt0) cc_final: 0.8398 (mp10) REVERT: H 281 TRP cc_start: 0.8625 (t60) cc_final: 0.8127 (t60) REVERT: H 438 TYR cc_start: 0.8363 (m-80) cc_final: 0.8083 (m-80) REVERT: H 440 ASN cc_start: 0.8865 (m-40) cc_final: 0.8574 (p0) REVERT: H 470 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8245 (mp0) REVERT: H 484 MET cc_start: 0.8071 (mpp) cc_final: 0.7672 (mpp) REVERT: H 521 LEU cc_start: 0.9499 (mm) cc_final: 0.9024 (mm) REVERT: H 605 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8753 (pt0) REVERT: H 611 GLN cc_start: 0.8258 (tp40) cc_final: 0.8051 (tp40) REVERT: H 684 PHE cc_start: 0.9042 (t80) cc_final: 0.8802 (t80) REVERT: H 737 PHE cc_start: 0.9086 (m-80) cc_final: 0.8702 (m-80) REVERT: I 35 HIS cc_start: 0.7814 (m90) cc_final: 0.7546 (m90) REVERT: I 149 TYR cc_start: 0.9098 (t80) cc_final: 0.8865 (t80) REVERT: I 157 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8203 (ttp80) REVERT: I 158 ASP cc_start: 0.9066 (m-30) cc_final: 0.8675 (m-30) REVERT: I 205 PHE cc_start: 0.8412 (m-80) cc_final: 0.8120 (m-10) REVERT: I 264 MET cc_start: 0.8780 (pmm) cc_final: 0.8433 (pmm) REVERT: I 267 ARG cc_start: 0.9020 (ptp90) cc_final: 0.8736 (ptt-90) REVERT: I 268 TYR cc_start: 0.8835 (t80) cc_final: 0.8434 (t80) REVERT: I 281 TRP cc_start: 0.8652 (t60) cc_final: 0.8386 (t60) REVERT: I 440 ASN cc_start: 0.7664 (m-40) cc_final: 0.7315 (m-40) REVERT: I 441 MET cc_start: 0.6469 (tmm) cc_final: 0.5161 (tmm) REVERT: I 597 GLU cc_start: 0.6751 (mp0) cc_final: 0.6291 (mp0) REVERT: J 64 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8636 (mm-30) REVERT: J 157 ARG cc_start: 0.8878 (ptt-90) cc_final: 0.8467 (ptt-90) REVERT: J 217 PHE cc_start: 0.9157 (t80) cc_final: 0.8697 (t80) REVERT: J 221 PHE cc_start: 0.8880 (t80) cc_final: 0.8295 (t80) REVERT: J 223 TYR cc_start: 0.8654 (m-80) cc_final: 0.8317 (m-80) REVERT: J 247 PHE cc_start: 0.9081 (m-80) cc_final: 0.8752 (m-80) REVERT: J 277 HIS cc_start: 0.9042 (t-90) cc_final: 0.8833 (t-90) REVERT: J 411 GLN cc_start: 0.8857 (tp-100) cc_final: 0.8495 (pt0) REVERT: J 436 TYR cc_start: 0.6888 (m-10) cc_final: 0.6531 (m-80) outliers start: 3 outliers final: 0 residues processed: 937 average time/residue: 0.5432 time to fit residues: 826.3063 Evaluate side-chains 813 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 811 time to evaluate : 4.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 458 optimal weight: 5.9990 chunk 312 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 410 optimal weight: 7.9990 chunk 227 optimal weight: 0.3980 chunk 470 optimal weight: 3.9990 chunk 380 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 281 optimal weight: 0.3980 chunk 494 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN A 557 GLN B 263 HIS ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 GLN B 697 ASN C 602 ASN D 263 HIS ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN E 299 HIS ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 GLN ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 594 ASN ** H 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 690 HIS ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 HIS J 186 GLN ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 42867 Z= 0.159 Angle : 0.584 8.987 58454 Z= 0.304 Chirality : 0.045 0.247 6899 Planarity : 0.004 0.064 7709 Dihedral : 4.591 22.881 6111 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.07 % Allowed : 2.47 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.55 (0.11), residues: 5708 helix: 0.23 (0.13), residues: 1620 sheet: -0.29 (0.16), residues: 1002 loop : -0.64 (0.11), residues: 3086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 271 HIS 0.005 0.001 HIS E 336 PHE 0.027 0.001 PHE I 471 TYR 0.042 0.001 TYR I 167 ARG 0.010 0.001 ARG C 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1069 time to evaluate : 5.241 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8194 (tm-30) REVERT: A 192 TYR cc_start: 0.8922 (p90) cc_final: 0.8497 (p90) REVERT: A 200 ARG cc_start: 0.7505 (mpt180) cc_final: 0.7020 (mpt-90) REVERT: A 250 GLU cc_start: 0.8885 (mp0) cc_final: 0.8542 (tp30) REVERT: A 324 PHE cc_start: 0.8341 (p90) cc_final: 0.7996 (p90) REVERT: A 391 LEU cc_start: 0.9116 (mm) cc_final: 0.8889 (mm) REVERT: A 436 TYR cc_start: 0.9095 (t80) cc_final: 0.8554 (t80) REVERT: A 453 ASP cc_start: 0.8794 (p0) cc_final: 0.7955 (p0) REVERT: A 479 GLU cc_start: 0.9174 (mp0) cc_final: 0.8706 (pm20) REVERT: A 490 ARG cc_start: 0.8574 (ptm160) cc_final: 0.7886 (ptm-80) REVERT: A 496 LYS cc_start: 0.9351 (mmtt) cc_final: 0.9097 (mmmt) REVERT: A 521 MET cc_start: 0.8890 (tmm) cc_final: 0.8683 (tmm) REVERT: A 525 GLU cc_start: 0.9327 (mp0) cc_final: 0.9059 (mp0) REVERT: A 551 ASP cc_start: 0.8415 (t0) cc_final: 0.7963 (p0) REVERT: A 552 PHE cc_start: 0.9185 (m-80) cc_final: 0.8701 (m-80) REVERT: A 569 LEU cc_start: 0.9327 (mm) cc_final: 0.9110 (mm) REVERT: A 590 LEU cc_start: 0.9320 (tt) cc_final: 0.9072 (tt) REVERT: A 727 PHE cc_start: 0.9044 (t80) cc_final: 0.8590 (t80) REVERT: B 185 ASP cc_start: 0.8550 (p0) cc_final: 0.8190 (p0) REVERT: B 190 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8159 (tm-30) REVERT: B 192 TYR cc_start: 0.9013 (p90) cc_final: 0.8019 (p90) REVERT: B 225 LYS cc_start: 0.9131 (tttm) cc_final: 0.8858 (tttt) REVERT: B 227 SER cc_start: 0.9305 (p) cc_final: 0.8863 (m) REVERT: B 243 ILE cc_start: 0.9045 (tt) cc_final: 0.8529 (pt) REVERT: B 244 ASP cc_start: 0.8593 (t70) cc_final: 0.7805 (t0) REVERT: B 246 ASN cc_start: 0.9183 (m110) cc_final: 0.8732 (m-40) REVERT: B 297 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8100 (ttp80) REVERT: B 328 ASN cc_start: 0.7764 (t0) cc_final: 0.7239 (t0) REVERT: B 438 GLN cc_start: 0.9381 (mt0) cc_final: 0.9081 (mt0) REVERT: B 439 PHE cc_start: 0.9406 (t80) cc_final: 0.9163 (t80) REVERT: B 470 ARG cc_start: 0.8148 (ptp90) cc_final: 0.7661 (ttp80) REVERT: B 504 ARG cc_start: 0.7655 (mtp180) cc_final: 0.7206 (mtp180) REVERT: B 515 GLU cc_start: 0.8445 (tp30) cc_final: 0.7738 (tp30) REVERT: B 552 PHE cc_start: 0.7336 (p90) cc_final: 0.7081 (p90) REVERT: B 557 GLN cc_start: 0.8066 (tp40) cc_final: 0.7755 (tp40) REVERT: B 561 ASN cc_start: 0.9027 (m110) cc_final: 0.8393 (m-40) REVERT: B 565 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8773 (mt0) REVERT: B 727 PHE cc_start: 0.8593 (t80) cc_final: 0.8226 (t80) REVERT: C 195 ASP cc_start: 0.8006 (t0) cc_final: 0.7630 (t0) REVERT: C 220 LYS cc_start: 0.8880 (mttt) cc_final: 0.8663 (mmtt) REVERT: C 243 ILE cc_start: 0.9358 (tp) cc_final: 0.9052 (tp) REVERT: C 259 TYR cc_start: 0.9020 (p90) cc_final: 0.8231 (p90) REVERT: C 326 ASN cc_start: 0.7936 (p0) cc_final: 0.7448 (p0) REVERT: C 328 ASN cc_start: 0.7077 (p0) cc_final: 0.6565 (p0) REVERT: C 336 HIS cc_start: 0.9050 (p-80) cc_final: 0.8516 (p-80) REVERT: C 434 MET cc_start: 0.9084 (ppp) cc_final: 0.8757 (ppp) REVERT: C 497 ASP cc_start: 0.8159 (p0) cc_final: 0.7897 (p0) REVERT: C 512 ASP cc_start: 0.8579 (t0) cc_final: 0.8019 (t0) REVERT: C 550 PHE cc_start: 0.9325 (m-80) cc_final: 0.8809 (m-80) REVERT: C 551 ASP cc_start: 0.8739 (t0) cc_final: 0.8477 (t70) REVERT: C 552 PHE cc_start: 0.8652 (m-80) cc_final: 0.8238 (m-80) REVERT: C 575 TYR cc_start: 0.7113 (m-80) cc_final: 0.6767 (m-80) REVERT: C 578 LEU cc_start: 0.9466 (pp) cc_final: 0.9212 (pp) REVERT: C 590 LEU cc_start: 0.9352 (tt) cc_final: 0.9066 (tt) REVERT: C 596 PHE cc_start: 0.8761 (m-80) cc_final: 0.7966 (m-80) REVERT: C 636 ARG cc_start: 0.8869 (ptt-90) cc_final: 0.8610 (ptp90) REVERT: C 727 PHE cc_start: 0.7949 (t80) cc_final: 0.7727 (t80) REVERT: D 192 TYR cc_start: 0.9020 (p90) cc_final: 0.8635 (p90) REVERT: D 195 ASP cc_start: 0.8240 (t0) cc_final: 0.7990 (t70) REVERT: D 226 TRP cc_start: 0.8121 (t60) cc_final: 0.7887 (t60) REVERT: D 299 HIS cc_start: 0.8848 (t-90) cc_final: 0.8618 (t-90) REVERT: D 365 ARG cc_start: 0.7925 (ttm-80) cc_final: 0.7196 (tpp-160) REVERT: D 408 ASN cc_start: 0.9188 (t0) cc_final: 0.8942 (t0) REVERT: D 441 GLU cc_start: 0.8897 (tp30) cc_final: 0.8582 (tp30) REVERT: D 447 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7562 (tm-30) REVERT: D 456 TYR cc_start: 0.9050 (m-10) cc_final: 0.8819 (m-10) REVERT: D 462 TYR cc_start: 0.8430 (t80) cc_final: 0.8221 (t80) REVERT: D 565 GLN cc_start: 0.9476 (mm-40) cc_final: 0.9015 (mt0) REVERT: D 638 ILE cc_start: 0.8995 (pt) cc_final: 0.8523 (pt) REVERT: D 703 LYS cc_start: 0.9569 (mppt) cc_final: 0.9228 (mmtm) REVERT: E 411 TYR cc_start: 0.8402 (t80) cc_final: 0.7736 (t80) REVERT: E 436 TYR cc_start: 0.8685 (t80) cc_final: 0.8040 (t80) REVERT: E 439 PHE cc_start: 0.9387 (t80) cc_final: 0.9180 (t80) REVERT: E 509 ASN cc_start: 0.9212 (t0) cc_final: 0.8849 (t0) REVERT: E 512 ASP cc_start: 0.7873 (t0) cc_final: 0.6267 (t0) REVERT: E 553 ASN cc_start: 0.8719 (m-40) cc_final: 0.8205 (m-40) REVERT: E 616 HIS cc_start: 0.8940 (m90) cc_final: 0.8648 (p-80) REVERT: F 176 PRO cc_start: 0.8458 (Cg_exo) cc_final: 0.8054 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8351 (tm-30) REVERT: F 223 PRO cc_start: 0.9396 (Cg_endo) cc_final: 0.9080 (Cg_exo) REVERT: F 226 TRP cc_start: 0.9312 (t60) cc_final: 0.9036 (t60) REVERT: F 265 ASP cc_start: 0.8889 (t0) cc_final: 0.8424 (p0) REVERT: F 326 ASN cc_start: 0.7875 (m-40) cc_final: 0.6007 (m-40) REVERT: F 332 VAL cc_start: 0.8149 (p) cc_final: 0.7888 (p) REVERT: F 439 PHE cc_start: 0.9563 (t80) cc_final: 0.9207 (t80) REVERT: F 442 LEU cc_start: 0.9704 (tt) cc_final: 0.9488 (pp) REVERT: F 453 ASP cc_start: 0.8835 (p0) cc_final: 0.8587 (p0) REVERT: F 490 ARG cc_start: 0.7919 (ttt180) cc_final: 0.7668 (ttp80) REVERT: F 501 VAL cc_start: 0.9171 (t) cc_final: 0.8910 (p) REVERT: F 551 ASP cc_start: 0.7521 (t0) cc_final: 0.6827 (p0) REVERT: F 602 ASN cc_start: 0.9294 (m-40) cc_final: 0.8929 (m110) REVERT: F 708 ILE cc_start: 0.9023 (pt) cc_final: 0.8746 (tp) REVERT: G 242 ARG cc_start: 0.8560 (mtt90) cc_final: 0.8009 (mmm-85) REVERT: G 266 MET cc_start: 0.8549 (ttt) cc_final: 0.8151 (ttt) REVERT: G 365 ARG cc_start: 0.7550 (mtt-85) cc_final: 0.7297 (mmt180) REVERT: G 439 PHE cc_start: 0.9296 (t80) cc_final: 0.9090 (t80) REVERT: G 440 LEU cc_start: 0.9169 (mt) cc_final: 0.8882 (mt) REVERT: G 512 ASP cc_start: 0.8318 (t0) cc_final: 0.6532 (t0) REVERT: G 514 LEU cc_start: 0.9517 (tt) cc_final: 0.9135 (tt) REVERT: G 551 ASP cc_start: 0.8866 (t0) cc_final: 0.7873 (p0) REVERT: G 552 PHE cc_start: 0.8915 (m-80) cc_final: 0.8619 (m-80) REVERT: G 561 ASN cc_start: 0.9517 (t0) cc_final: 0.9305 (t0) REVERT: G 569 LEU cc_start: 0.9273 (mt) cc_final: 0.9061 (mt) REVERT: G 582 LYS cc_start: 0.9382 (mmtm) cc_final: 0.9147 (mmmt) REVERT: G 638 ILE cc_start: 0.9024 (pt) cc_final: 0.8040 (mm) REVERT: G 727 PHE cc_start: 0.8192 (t80) cc_final: 0.7776 (t80) REVERT: H 65 LYS cc_start: 0.9537 (mmpt) cc_final: 0.9273 (mmtm) REVERT: H 145 LEU cc_start: 0.9141 (mt) cc_final: 0.8842 (mt) REVERT: H 150 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8382 (mm-30) REVERT: H 170 PHE cc_start: 0.9279 (t80) cc_final: 0.8610 (t80) REVERT: H 174 LEU cc_start: 0.9620 (mt) cc_final: 0.9398 (mt) REVERT: H 200 ASP cc_start: 0.9352 (p0) cc_final: 0.9118 (p0) REVERT: H 234 GLN cc_start: 0.8941 (mt0) cc_final: 0.8419 (mp10) REVERT: H 281 TRP cc_start: 0.8660 (t60) cc_final: 0.7820 (t60) REVERT: H 390 GLN cc_start: 0.8816 (mp10) cc_final: 0.8610 (mp10) REVERT: H 438 TYR cc_start: 0.8307 (m-80) cc_final: 0.7990 (m-80) REVERT: H 441 MET cc_start: 0.8153 (tmm) cc_final: 0.7531 (tmm) REVERT: H 470 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8203 (mp0) REVERT: H 484 MET cc_start: 0.8183 (mpp) cc_final: 0.7778 (mpp) REVERT: H 486 VAL cc_start: 0.8797 (m) cc_final: 0.8546 (p) REVERT: H 499 LEU cc_start: 0.8811 (mp) cc_final: 0.7885 (mp) REVERT: H 521 LEU cc_start: 0.9505 (mm) cc_final: 0.9031 (mm) REVERT: H 527 LEU cc_start: 0.8447 (mt) cc_final: 0.8191 (mm) REVERT: H 568 GLN cc_start: 0.8758 (pp30) cc_final: 0.6455 (pp30) REVERT: H 582 LEU cc_start: 0.8826 (pp) cc_final: 0.8291 (mm) REVERT: H 605 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8750 (pt0) REVERT: H 611 GLN cc_start: 0.8362 (tp40) cc_final: 0.8096 (tp40) REVERT: H 736 PHE cc_start: 0.8866 (t80) cc_final: 0.8457 (t80) REVERT: H 737 PHE cc_start: 0.9082 (m-80) cc_final: 0.8499 (m-80) REVERT: I 35 HIS cc_start: 0.7904 (m90) cc_final: 0.7598 (m90) REVERT: I 154 ILE cc_start: 0.9255 (mm) cc_final: 0.9022 (mm) REVERT: I 157 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8084 (ttp80) REVERT: I 205 PHE cc_start: 0.8352 (m-80) cc_final: 0.7941 (m-80) REVERT: I 230 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.7938 (ttm170) REVERT: I 254 LEU cc_start: 0.8384 (pp) cc_final: 0.8123 (mm) REVERT: I 264 MET cc_start: 0.8803 (pmm) cc_final: 0.7713 (pmm) REVERT: I 277 HIS cc_start: 0.7679 (t70) cc_final: 0.7435 (t70) REVERT: I 281 TRP cc_start: 0.8610 (t60) cc_final: 0.8335 (t60) REVERT: I 441 MET cc_start: 0.6673 (tmm) cc_final: 0.5538 (tmm) REVERT: I 597 GLU cc_start: 0.6867 (mp0) cc_final: 0.6508 (mp0) REVERT: J 64 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8730 (mm-30) REVERT: J 153 LYS cc_start: 0.9221 (ttmm) cc_final: 0.8983 (mtmm) REVERT: J 157 ARG cc_start: 0.8829 (ptt-90) cc_final: 0.8447 (ptt-90) REVERT: J 174 LEU cc_start: 0.8843 (mm) cc_final: 0.8317 (pp) REVERT: J 201 PHE cc_start: 0.8797 (m-80) cc_final: 0.7596 (m-80) REVERT: J 217 PHE cc_start: 0.9142 (t80) cc_final: 0.8693 (t80) REVERT: J 221 PHE cc_start: 0.8878 (t80) cc_final: 0.8303 (t80) REVERT: J 223 TYR cc_start: 0.8637 (m-80) cc_final: 0.8237 (m-80) REVERT: J 247 PHE cc_start: 0.9076 (m-80) cc_final: 0.8666 (m-10) REVERT: J 277 HIS cc_start: 0.9026 (t-90) cc_final: 0.8781 (t-90) REVERT: J 411 GLN cc_start: 0.8856 (tp-100) cc_final: 0.8505 (pt0) REVERT: J 436 TYR cc_start: 0.6925 (m-10) cc_final: 0.6539 (m-80) outliers start: 3 outliers final: 1 residues processed: 1072 average time/residue: 0.5741 time to fit residues: 1017.9691 Evaluate side-chains 864 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 863 time to evaluate : 5.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 185 optimal weight: 0.5980 chunk 496 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 323 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 551 optimal weight: 50.0000 chunk 457 optimal weight: 3.9990 chunk 255 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 182 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 HIS B 697 ASN C 263 HIS C 299 HIS C 602 ASN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 HIS E 483 GLN ** E 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 556 GLN G 198 ASN ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 447 GLN G 454 GLN ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 594 ASN H 604 ASN ** H 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 HIS ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.165 42867 Z= 0.407 Angle : 0.685 10.911 58454 Z= 0.360 Chirality : 0.046 0.302 6899 Planarity : 0.005 0.115 7709 Dihedral : 4.931 22.453 6111 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.05 % Allowed : 2.64 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.72 (0.11), residues: 5708 helix: 0.07 (0.13), residues: 1635 sheet: -0.34 (0.16), residues: 1036 loop : -0.76 (0.11), residues: 3037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 271 HIS 0.009 0.002 HIS F 253 PHE 0.023 0.002 PHE B 531 TYR 0.034 0.002 TYR I 149 ARG 0.018 0.001 ARG H 391 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 927 time to evaluate : 4.972 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8241 (tm-30) REVERT: A 192 TYR cc_start: 0.9069 (p90) cc_final: 0.8674 (p90) REVERT: A 200 ARG cc_start: 0.7577 (mpt180) cc_final: 0.7102 (mpt-90) REVERT: A 225 LYS cc_start: 0.8763 (ttpt) cc_final: 0.8525 (ttpt) REVERT: A 324 PHE cc_start: 0.8364 (p90) cc_final: 0.7990 (p90) REVERT: A 391 LEU cc_start: 0.9215 (mm) cc_final: 0.9001 (mm) REVERT: A 415 ASN cc_start: 0.8756 (m110) cc_final: 0.8445 (m110) REVERT: A 436 TYR cc_start: 0.9124 (t80) cc_final: 0.8570 (t80) REVERT: A 439 PHE cc_start: 0.9409 (t80) cc_final: 0.9204 (t80) REVERT: A 453 ASP cc_start: 0.8909 (p0) cc_final: 0.8062 (p0) REVERT: A 479 GLU cc_start: 0.9272 (mp0) cc_final: 0.8739 (mp0) REVERT: A 490 ARG cc_start: 0.8690 (ptm160) cc_final: 0.8276 (ptm-80) REVERT: A 525 GLU cc_start: 0.9333 (mp0) cc_final: 0.9072 (mp0) REVERT: A 569 LEU cc_start: 0.9349 (mm) cc_final: 0.9104 (mm) REVERT: A 727 PHE cc_start: 0.9011 (t80) cc_final: 0.8625 (t80) REVERT: B 185 ASP cc_start: 0.8700 (p0) cc_final: 0.8368 (p0) REVERT: B 190 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8221 (tm-30) REVERT: B 192 TYR cc_start: 0.9017 (p90) cc_final: 0.8273 (p90) REVERT: B 225 LYS cc_start: 0.9168 (tttm) cc_final: 0.8919 (tttt) REVERT: B 227 SER cc_start: 0.9132 (p) cc_final: 0.8760 (m) REVERT: B 244 ASP cc_start: 0.8573 (t70) cc_final: 0.7988 (t0) REVERT: B 246 ASN cc_start: 0.9089 (m110) cc_final: 0.8530 (m110) REVERT: B 328 ASN cc_start: 0.7543 (t0) cc_final: 0.7021 (t0) REVERT: B 470 ARG cc_start: 0.8347 (ptp90) cc_final: 0.7554 (ttp80) REVERT: B 478 SER cc_start: 0.9521 (m) cc_final: 0.9255 (p) REVERT: B 512 ASP cc_start: 0.8267 (t0) cc_final: 0.8049 (t0) REVERT: B 561 ASN cc_start: 0.9048 (m110) cc_final: 0.8658 (m110) REVERT: B 565 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8757 (mt0) REVERT: B 727 PHE cc_start: 0.8574 (t80) cc_final: 0.8331 (t80) REVERT: C 185 ASP cc_start: 0.8845 (p0) cc_final: 0.8474 (p0) REVERT: C 195 ASP cc_start: 0.7921 (t0) cc_final: 0.7561 (t0) REVERT: C 233 TYR cc_start: 0.8030 (m-10) cc_final: 0.7769 (m-10) REVERT: C 326 ASN cc_start: 0.7957 (p0) cc_final: 0.7586 (p0) REVERT: C 336 HIS cc_start: 0.9084 (p-80) cc_final: 0.8538 (p-80) REVERT: C 343 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7430 (mp0) REVERT: C 434 MET cc_start: 0.8995 (ppp) cc_final: 0.8747 (ppp) REVERT: C 476 ASN cc_start: 0.9201 (p0) cc_final: 0.8773 (p0) REVERT: C 497 ASP cc_start: 0.8212 (p0) cc_final: 0.7945 (p0) REVERT: C 528 LYS cc_start: 0.9150 (ttmm) cc_final: 0.8660 (mmtt) REVERT: C 552 PHE cc_start: 0.8726 (m-80) cc_final: 0.8371 (m-80) REVERT: C 575 TYR cc_start: 0.7248 (m-80) cc_final: 0.6734 (m-80) REVERT: C 590 LEU cc_start: 0.9325 (tt) cc_final: 0.9008 (tt) REVERT: C 596 PHE cc_start: 0.9006 (m-80) cc_final: 0.8385 (m-80) REVERT: C 721 ILE cc_start: 0.8157 (mp) cc_final: 0.7597 (mp) REVERT: C 727 PHE cc_start: 0.7919 (t80) cc_final: 0.7557 (t80) REVERT: D 195 ASP cc_start: 0.8295 (t0) cc_final: 0.8046 (t70) REVERT: D 367 VAL cc_start: 0.9450 (t) cc_final: 0.9078 (p) REVERT: D 408 ASN cc_start: 0.9193 (t0) cc_final: 0.8859 (t0) REVERT: D 437 ASN cc_start: 0.9535 (m-40) cc_final: 0.9180 (m-40) REVERT: D 447 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7604 (tm-30) REVERT: D 456 TYR cc_start: 0.9095 (m-10) cc_final: 0.8895 (m-10) REVERT: D 525 GLU cc_start: 0.8924 (mp0) cc_final: 0.8658 (mp0) REVERT: D 565 GLN cc_start: 0.9451 (mm-40) cc_final: 0.9031 (mt0) REVERT: D 617 ARG cc_start: 0.8994 (ptp-110) cc_final: 0.8751 (ptp-110) REVERT: D 703 LYS cc_start: 0.9514 (mppt) cc_final: 0.9257 (mmtm) REVERT: E 202 PHE cc_start: 0.8474 (t80) cc_final: 0.8129 (t80) REVERT: E 299 HIS cc_start: 0.8711 (t70) cc_final: 0.8355 (t-90) REVERT: E 421 LEU cc_start: 0.9502 (mt) cc_final: 0.9298 (mt) REVERT: E 436 TYR cc_start: 0.8725 (t80) cc_final: 0.8371 (t80) REVERT: E 509 ASN cc_start: 0.9238 (t0) cc_final: 0.8900 (t0) REVERT: E 512 ASP cc_start: 0.8189 (t0) cc_final: 0.6431 (t0) REVERT: E 553 ASN cc_start: 0.8898 (m-40) cc_final: 0.8411 (m-40) REVERT: E 639 LEU cc_start: 0.9541 (mm) cc_final: 0.9112 (tp) REVERT: F 176 PRO cc_start: 0.8684 (Cg_exo) cc_final: 0.8417 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8306 (tm-30) REVERT: F 223 PRO cc_start: 0.9395 (Cg_endo) cc_final: 0.8972 (Cg_exo) REVERT: F 226 TRP cc_start: 0.9434 (t60) cc_final: 0.9148 (t-100) REVERT: F 242 ARG cc_start: 0.7888 (mtp180) cc_final: 0.7517 (mtp180) REVERT: F 265 ASP cc_start: 0.8861 (t0) cc_final: 0.8489 (p0) REVERT: F 326 ASN cc_start: 0.7983 (m-40) cc_final: 0.7436 (m-40) REVERT: F 366 TYR cc_start: 0.8905 (m-10) cc_final: 0.8562 (m-10) REVERT: F 439 PHE cc_start: 0.9561 (t80) cc_final: 0.9289 (t80) REVERT: F 453 ASP cc_start: 0.8906 (p0) cc_final: 0.8600 (p0) REVERT: F 497 ASP cc_start: 0.8785 (p0) cc_final: 0.8446 (p0) REVERT: F 501 VAL cc_start: 0.9251 (t) cc_final: 0.8986 (p) REVERT: F 512 ASP cc_start: 0.7989 (m-30) cc_final: 0.7712 (m-30) REVERT: F 521 MET cc_start: 0.7634 (pmm) cc_final: 0.7143 (pmm) REVERT: F 523 LEU cc_start: 0.9443 (tp) cc_final: 0.9220 (tp) REVERT: F 551 ASP cc_start: 0.7555 (t0) cc_final: 0.6792 (p0) REVERT: F 602 ASN cc_start: 0.9333 (m-40) cc_final: 0.8779 (m110) REVERT: G 365 ARG cc_start: 0.7671 (mtt-85) cc_final: 0.7192 (mmt180) REVERT: G 448 LEU cc_start: 0.9536 (mm) cc_final: 0.9238 (mm) REVERT: G 550 PHE cc_start: 0.8181 (m-80) cc_final: 0.7510 (m-80) REVERT: G 551 ASP cc_start: 0.8986 (t0) cc_final: 0.7921 (p0) REVERT: G 552 PHE cc_start: 0.8956 (m-80) cc_final: 0.8648 (m-80) REVERT: G 582 LYS cc_start: 0.9389 (mmtm) cc_final: 0.9181 (mmmt) REVERT: G 583 LEU cc_start: 0.9417 (mt) cc_final: 0.8585 (mt) REVERT: G 587 MET cc_start: 0.9388 (ptp) cc_final: 0.9098 (ptp) REVERT: G 596 PHE cc_start: 0.9249 (m-80) cc_final: 0.8969 (m-80) REVERT: G 638 ILE cc_start: 0.9136 (pt) cc_final: 0.8309 (mm) REVERT: G 727 PHE cc_start: 0.8183 (t80) cc_final: 0.7664 (t80) REVERT: H 145 LEU cc_start: 0.9195 (mt) cc_final: 0.8901 (mt) REVERT: H 158 ASP cc_start: 0.9418 (t0) cc_final: 0.9147 (m-30) REVERT: H 170 PHE cc_start: 0.9331 (t80) cc_final: 0.8705 (t80) REVERT: H 174 LEU cc_start: 0.9669 (mt) cc_final: 0.9410 (mt) REVERT: H 200 ASP cc_start: 0.9371 (p0) cc_final: 0.9121 (p0) REVERT: H 234 GLN cc_start: 0.8961 (mt0) cc_final: 0.8469 (mp10) REVERT: H 235 LEU cc_start: 0.9309 (mm) cc_final: 0.9055 (mm) REVERT: H 281 TRP cc_start: 0.8697 (t60) cc_final: 0.8010 (t60) REVERT: H 390 GLN cc_start: 0.8789 (mp10) cc_final: 0.8536 (mp10) REVERT: H 438 TYR cc_start: 0.8414 (m-80) cc_final: 0.8163 (m-80) REVERT: H 441 MET cc_start: 0.8229 (tmm) cc_final: 0.7799 (tmm) REVERT: H 484 MET cc_start: 0.8129 (mpp) cc_final: 0.7843 (mpp) REVERT: H 499 LEU cc_start: 0.8704 (mp) cc_final: 0.7587 (mp) REVERT: H 521 LEU cc_start: 0.9508 (mm) cc_final: 0.9072 (mm) REVERT: H 568 GLN cc_start: 0.8698 (pp30) cc_final: 0.6841 (pt0) REVERT: H 611 GLN cc_start: 0.8335 (tp40) cc_final: 0.8082 (tp40) REVERT: H 736 PHE cc_start: 0.8876 (t80) cc_final: 0.8521 (t80) REVERT: H 737 PHE cc_start: 0.9129 (m-80) cc_final: 0.8545 (m-80) REVERT: I 35 HIS cc_start: 0.7657 (m90) cc_final: 0.7395 (m90) REVERT: I 108 TYR cc_start: 0.8232 (m-10) cc_final: 0.8012 (m-10) REVERT: I 149 TYR cc_start: 0.9252 (t80) cc_final: 0.8996 (t80) REVERT: I 205 PHE cc_start: 0.8408 (m-80) cc_final: 0.8130 (m-10) REVERT: I 230 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8259 (ttm170) REVERT: I 244 MET cc_start: 0.9531 (tpt) cc_final: 0.9320 (tpt) REVERT: I 260 LYS cc_start: 0.9382 (mmpt) cc_final: 0.9167 (mmmt) REVERT: I 264 MET cc_start: 0.8012 (pmm) cc_final: 0.7765 (pmm) REVERT: I 267 ARG cc_start: 0.8978 (ptp90) cc_final: 0.8718 (ptt-90) REVERT: I 281 TRP cc_start: 0.8641 (t60) cc_final: 0.8326 (t60) REVERT: I 440 ASN cc_start: 0.7602 (m-40) cc_final: 0.7269 (m-40) REVERT: I 597 GLU cc_start: 0.6995 (mp0) cc_final: 0.6546 (mp0) REVERT: J 64 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8729 (mm-30) REVERT: J 153 LYS cc_start: 0.9208 (ttmm) cc_final: 0.8972 (mtmm) REVERT: J 157 ARG cc_start: 0.8849 (ptt-90) cc_final: 0.8463 (ptt-90) REVERT: J 170 PHE cc_start: 0.8251 (t80) cc_final: 0.7755 (t80) REVERT: J 201 PHE cc_start: 0.8793 (m-80) cc_final: 0.8219 (m-80) REVERT: J 205 PHE cc_start: 0.8915 (m-80) cc_final: 0.8485 (m-80) REVERT: J 221 PHE cc_start: 0.8894 (t80) cc_final: 0.8381 (t80) REVERT: J 223 TYR cc_start: 0.8680 (m-80) cc_final: 0.8354 (m-80) REVERT: J 247 PHE cc_start: 0.9120 (m-80) cc_final: 0.8700 (m-10) REVERT: J 411 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8514 (pt0) REVERT: J 436 TYR cc_start: 0.6893 (m-10) cc_final: 0.6551 (m-80) outliers start: 2 outliers final: 0 residues processed: 929 average time/residue: 0.5283 time to fit residues: 796.5869 Evaluate side-chains 794 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 794 time to evaluate : 5.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 531 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 314 optimal weight: 1.9990 chunk 402 optimal weight: 7.9990 chunk 312 optimal weight: 0.2980 chunk 464 optimal weight: 50.0000 chunk 307 optimal weight: 0.0020 chunk 549 optimal weight: 50.0000 chunk 343 optimal weight: 0.5980 chunk 334 optimal weight: 0.0040 chunk 253 optimal weight: 30.0000 overall best weight: 0.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 HIS A 630 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 594 ASN J 117 HIS ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 405 ASN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 42867 Z= 0.159 Angle : 0.588 9.325 58454 Z= 0.304 Chirality : 0.045 0.221 6899 Planarity : 0.004 0.052 7709 Dihedral : 4.541 23.850 6111 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.02 % Allowed : 1.58 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.47 (0.11), residues: 5708 helix: 0.33 (0.13), residues: 1599 sheet: -0.15 (0.16), residues: 1047 loop : -0.65 (0.11), residues: 3062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 271 HIS 0.006 0.001 HIS E 336 PHE 0.025 0.001 PHE C 439 TYR 0.027 0.001 TYR H 591 ARG 0.009 0.001 ARG C 468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1047 time to evaluate : 4.907 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8170 (tm-30) REVERT: A 192 TYR cc_start: 0.8864 (p90) cc_final: 0.8469 (p90) REVERT: A 200 ARG cc_start: 0.7471 (mpt180) cc_final: 0.7041 (mpt-90) REVERT: A 324 PHE cc_start: 0.8234 (p90) cc_final: 0.7775 (p90) REVERT: A 391 LEU cc_start: 0.9179 (mm) cc_final: 0.8936 (mm) REVERT: A 415 ASN cc_start: 0.8696 (m110) cc_final: 0.8488 (m110) REVERT: A 436 TYR cc_start: 0.9072 (t80) cc_final: 0.8533 (t80) REVERT: A 453 ASP cc_start: 0.8891 (p0) cc_final: 0.8297 (p0) REVERT: A 456 TYR cc_start: 0.8515 (m-10) cc_final: 0.8240 (m-10) REVERT: A 465 GLU cc_start: 0.8529 (mp0) cc_final: 0.8209 (pm20) REVERT: A 490 ARG cc_start: 0.8682 (ptm160) cc_final: 0.8262 (ptm-80) REVERT: A 496 LYS cc_start: 0.9297 (mmtt) cc_final: 0.9073 (mmmt) REVERT: A 525 GLU cc_start: 0.9304 (mp0) cc_final: 0.9036 (mp0) REVERT: A 552 PHE cc_start: 0.9168 (m-80) cc_final: 0.8866 (m-80) REVERT: A 631 ILE cc_start: 0.8990 (mp) cc_final: 0.8471 (tp) REVERT: A 635 ILE cc_start: 0.9603 (mm) cc_final: 0.9368 (mm) REVERT: A 727 PHE cc_start: 0.9037 (t80) cc_final: 0.8608 (t80) REVERT: B 185 ASP cc_start: 0.8538 (p0) cc_final: 0.8241 (p0) REVERT: B 190 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8053 (tm-30) REVERT: B 192 TYR cc_start: 0.8906 (p90) cc_final: 0.7938 (p90) REVERT: B 227 SER cc_start: 0.9255 (p) cc_final: 0.8794 (m) REVERT: B 244 ASP cc_start: 0.8618 (t70) cc_final: 0.8198 (t0) REVERT: B 246 ASN cc_start: 0.9130 (m110) cc_final: 0.8711 (m-40) REVERT: B 328 ASN cc_start: 0.7581 (t0) cc_final: 0.7087 (t0) REVERT: B 438 GLN cc_start: 0.9371 (mt0) cc_final: 0.9085 (mt0) REVERT: B 470 ARG cc_start: 0.8159 (ptp90) cc_final: 0.7040 (ttp80) REVERT: B 480 VAL cc_start: 0.9635 (p) cc_final: 0.9366 (m) REVERT: B 483 GLN cc_start: 0.9072 (mp10) cc_final: 0.8795 (mp10) REVERT: B 487 THR cc_start: 0.9406 (t) cc_final: 0.9163 (t) REVERT: B 504 ARG cc_start: 0.7217 (mmm-85) cc_final: 0.6760 (mmm-85) REVERT: B 512 ASP cc_start: 0.8229 (t0) cc_final: 0.7960 (t0) REVERT: B 515 GLU cc_start: 0.7646 (tp30) cc_final: 0.7206 (tm-30) REVERT: B 557 GLN cc_start: 0.7863 (tp40) cc_final: 0.7101 (tp40) REVERT: B 560 GLN cc_start: 0.9340 (tm-30) cc_final: 0.9080 (tm-30) REVERT: B 561 ASN cc_start: 0.9064 (m110) cc_final: 0.8379 (m110) REVERT: B 565 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8727 (mt0) REVERT: B 727 PHE cc_start: 0.8572 (t80) cc_final: 0.8286 (t80) REVERT: C 185 ASP cc_start: 0.8630 (p0) cc_final: 0.8368 (p0) REVERT: C 195 ASP cc_start: 0.7841 (t0) cc_final: 0.7409 (t0) REVERT: C 220 LYS cc_start: 0.8882 (mttt) cc_final: 0.8600 (mmtt) REVERT: C 224 GLU cc_start: 0.8050 (mp0) cc_final: 0.7749 (mp0) REVERT: C 243 ILE cc_start: 0.9418 (tp) cc_final: 0.8813 (tp) REVERT: C 244 ASP cc_start: 0.8715 (t0) cc_final: 0.8297 (t70) REVERT: C 328 ASN cc_start: 0.7313 (p0) cc_final: 0.6756 (p0) REVERT: C 336 HIS cc_start: 0.9038 (p-80) cc_final: 0.8470 (p-80) REVERT: C 343 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7366 (mp0) REVERT: C 434 MET cc_start: 0.9016 (ppp) cc_final: 0.8767 (ppp) REVERT: C 479 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8208 (mt-10) REVERT: C 497 ASP cc_start: 0.8188 (p0) cc_final: 0.7901 (p0) REVERT: C 512 ASP cc_start: 0.8532 (t0) cc_final: 0.7930 (t0) REVERT: C 528 LYS cc_start: 0.9110 (ttmm) cc_final: 0.8589 (mmtt) REVERT: C 550 PHE cc_start: 0.9331 (m-80) cc_final: 0.8808 (m-80) REVERT: C 552 PHE cc_start: 0.8722 (m-80) cc_final: 0.8297 (m-80) REVERT: C 575 TYR cc_start: 0.7150 (m-80) cc_final: 0.6667 (m-80) REVERT: C 590 LEU cc_start: 0.9303 (tt) cc_final: 0.9004 (tt) REVERT: C 596 PHE cc_start: 0.8966 (m-80) cc_final: 0.8467 (m-80) REVERT: C 727 PHE cc_start: 0.8006 (t80) cc_final: 0.7763 (t80) REVERT: D 192 TYR cc_start: 0.9018 (p90) cc_final: 0.8565 (p90) REVERT: D 195 ASP cc_start: 0.8194 (t0) cc_final: 0.7932 (t70) REVERT: D 263 HIS cc_start: 0.8241 (p-80) cc_final: 0.8023 (p90) REVERT: D 299 HIS cc_start: 0.8890 (t-90) cc_final: 0.8437 (t-90) REVERT: D 408 ASN cc_start: 0.9202 (t0) cc_final: 0.8923 (t0) REVERT: D 441 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8891 (pt0) REVERT: D 447 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7644 (tm-30) REVERT: D 468 ARG cc_start: 0.9079 (ttm110) cc_final: 0.8645 (ttp-110) REVERT: D 525 GLU cc_start: 0.8915 (mp0) cc_final: 0.8626 (mp0) REVERT: D 554 PHE cc_start: 0.8811 (m-80) cc_final: 0.8185 (m-80) REVERT: D 565 GLN cc_start: 0.9437 (mm-40) cc_final: 0.9092 (mt0) REVERT: D 617 ARG cc_start: 0.8973 (ptp-110) cc_final: 0.8767 (ptp-110) REVERT: D 703 LYS cc_start: 0.9556 (mppt) cc_final: 0.9278 (mmtm) REVERT: E 202 PHE cc_start: 0.8420 (t80) cc_final: 0.8088 (t80) REVERT: E 216 LEU cc_start: 0.9208 (mt) cc_final: 0.9003 (mt) REVERT: E 299 HIS cc_start: 0.8795 (t70) cc_final: 0.8520 (t-90) REVERT: E 411 TYR cc_start: 0.8546 (t80) cc_final: 0.7880 (t80) REVERT: E 436 TYR cc_start: 0.8682 (t80) cc_final: 0.8041 (t80) REVERT: E 439 PHE cc_start: 0.9422 (t80) cc_final: 0.9217 (t80) REVERT: E 509 ASN cc_start: 0.9247 (t0) cc_final: 0.8894 (t0) REVERT: E 512 ASP cc_start: 0.7915 (t0) cc_final: 0.7643 (t0) REVERT: E 553 ASN cc_start: 0.8661 (m-40) cc_final: 0.8100 (m-40) REVERT: E 616 HIS cc_start: 0.8942 (m90) cc_final: 0.8555 (m90) REVERT: F 176 PRO cc_start: 0.8656 (Cg_exo) cc_final: 0.8384 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8349 (tm-30) REVERT: F 216 LEU cc_start: 0.8824 (mp) cc_final: 0.8613 (mt) REVERT: F 223 PRO cc_start: 0.9361 (Cg_endo) cc_final: 0.9046 (Cg_exo) REVERT: F 226 TRP cc_start: 0.9356 (t60) cc_final: 0.9142 (t-100) REVERT: F 236 PHE cc_start: 0.8829 (t80) cc_final: 0.8606 (t80) REVERT: F 242 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7596 (mtp180) REVERT: F 265 ASP cc_start: 0.8853 (t0) cc_final: 0.8299 (p0) REVERT: F 326 ASN cc_start: 0.7723 (m-40) cc_final: 0.6248 (m-40) REVERT: F 366 TYR cc_start: 0.8661 (m-10) cc_final: 0.8398 (m-10) REVERT: F 439 PHE cc_start: 0.9583 (t80) cc_final: 0.9268 (t80) REVERT: F 453 ASP cc_start: 0.8791 (p0) cc_final: 0.8549 (p0) REVERT: F 480 VAL cc_start: 0.8456 (t) cc_final: 0.7997 (m) REVERT: F 490 ARG cc_start: 0.8057 (ttt180) cc_final: 0.7692 (ttp80) REVERT: F 501 VAL cc_start: 0.9156 (t) cc_final: 0.8896 (p) REVERT: F 521 MET cc_start: 0.7503 (pmm) cc_final: 0.7065 (pmm) REVERT: F 523 LEU cc_start: 0.9394 (tp) cc_final: 0.9089 (tp) REVERT: F 551 ASP cc_start: 0.7540 (t0) cc_final: 0.6795 (p0) REVERT: F 602 ASN cc_start: 0.9261 (m-40) cc_final: 0.8824 (m110) REVERT: G 246 ASN cc_start: 0.8197 (t0) cc_final: 0.7966 (t0) REVERT: G 334 ILE cc_start: 0.8625 (mp) cc_final: 0.8095 (tp) REVERT: G 365 ARG cc_start: 0.7566 (mtt-85) cc_final: 0.7186 (mmt180) REVERT: G 448 LEU cc_start: 0.9571 (mm) cc_final: 0.9244 (mm) REVERT: G 456 TYR cc_start: 0.9007 (m-10) cc_final: 0.8684 (m-10) REVERT: G 512 ASP cc_start: 0.8583 (t0) cc_final: 0.6880 (t0) REVERT: G 514 LEU cc_start: 0.9545 (tt) cc_final: 0.9029 (tt) REVERT: G 515 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8327 (mm-30) REVERT: G 550 PHE cc_start: 0.8069 (m-80) cc_final: 0.7427 (m-80) REVERT: G 551 ASP cc_start: 0.8905 (t0) cc_final: 0.7808 (p0) REVERT: G 552 PHE cc_start: 0.8910 (m-80) cc_final: 0.8652 (m-80) REVERT: G 561 ASN cc_start: 0.9503 (t0) cc_final: 0.9289 (t0) REVERT: G 569 LEU cc_start: 0.9230 (mt) cc_final: 0.8941 (mt) REVERT: G 582 LYS cc_start: 0.9361 (mmtm) cc_final: 0.9114 (mmtt) REVERT: G 583 LEU cc_start: 0.9375 (mt) cc_final: 0.9041 (mm) REVERT: G 596 PHE cc_start: 0.9167 (m-80) cc_final: 0.8912 (m-80) REVERT: G 638 ILE cc_start: 0.9069 (pt) cc_final: 0.8057 (mm) REVERT: G 727 PHE cc_start: 0.8188 (t80) cc_final: 0.7706 (t80) REVERT: H 65 LYS cc_start: 0.9552 (mmpt) cc_final: 0.9288 (mmtm) REVERT: H 145 LEU cc_start: 0.9158 (mt) cc_final: 0.8817 (mt) REVERT: H 158 ASP cc_start: 0.9372 (t0) cc_final: 0.9116 (m-30) REVERT: H 170 PHE cc_start: 0.9318 (t80) cc_final: 0.8638 (t80) REVERT: H 174 LEU cc_start: 0.9606 (mt) cc_final: 0.9384 (mt) REVERT: H 200 ASP cc_start: 0.9331 (p0) cc_final: 0.9095 (p0) REVERT: H 217 PHE cc_start: 0.8799 (t80) cc_final: 0.8354 (t80) REVERT: H 234 GLN cc_start: 0.8938 (mt0) cc_final: 0.8403 (mp10) REVERT: H 281 TRP cc_start: 0.8711 (t60) cc_final: 0.7880 (t60) REVERT: H 390 GLN cc_start: 0.8750 (mp10) cc_final: 0.8550 (mp10) REVERT: H 438 TYR cc_start: 0.8436 (m-80) cc_final: 0.8160 (m-80) REVERT: H 441 MET cc_start: 0.8088 (tmm) cc_final: 0.7521 (tmm) REVERT: H 470 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8199 (mp0) REVERT: H 484 MET cc_start: 0.8198 (mpp) cc_final: 0.7792 (mpp) REVERT: H 486 VAL cc_start: 0.8822 (m) cc_final: 0.8560 (p) REVERT: H 499 LEU cc_start: 0.8723 (mp) cc_final: 0.7571 (mp) REVERT: H 521 LEU cc_start: 0.9474 (mm) cc_final: 0.9019 (mm) REVERT: H 568 GLN cc_start: 0.8627 (pp30) cc_final: 0.6318 (pp30) REVERT: H 591 TYR cc_start: 0.8256 (t80) cc_final: 0.7667 (t80) REVERT: H 605 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8768 (pt0) REVERT: H 611 GLN cc_start: 0.8310 (tp40) cc_final: 0.8034 (tp40) REVERT: H 736 PHE cc_start: 0.8931 (t80) cc_final: 0.8513 (t80) REVERT: H 737 PHE cc_start: 0.9111 (m-80) cc_final: 0.8685 (m-80) REVERT: H 739 GLU cc_start: 0.8654 (mp0) cc_final: 0.8350 (mp0) REVERT: I 35 HIS cc_start: 0.7590 (m90) cc_final: 0.7361 (m90) REVERT: I 154 ILE cc_start: 0.9214 (mm) cc_final: 0.8905 (mm) REVERT: I 158 ASP cc_start: 0.8901 (m-30) cc_final: 0.8571 (m-30) REVERT: I 205 PHE cc_start: 0.8309 (m-80) cc_final: 0.7890 (m-80) REVERT: I 230 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.7997 (ttm110) REVERT: I 244 MET cc_start: 0.9525 (tpt) cc_final: 0.9223 (tpt) REVERT: I 254 LEU cc_start: 0.8467 (pp) cc_final: 0.8175 (mm) REVERT: I 264 MET cc_start: 0.8381 (pmm) cc_final: 0.7708 (pmm) REVERT: I 267 ARG cc_start: 0.8994 (ptp90) cc_final: 0.8727 (ptt-90) REVERT: I 268 TYR cc_start: 0.8973 (m-10) cc_final: 0.8768 (m-80) REVERT: I 281 TRP cc_start: 0.8489 (t60) cc_final: 0.8176 (t60) REVERT: I 440 ASN cc_start: 0.7578 (m-40) cc_final: 0.7231 (m-40) REVERT: I 441 MET cc_start: 0.6022 (tmm) cc_final: 0.5038 (tmm) REVERT: I 597 GLU cc_start: 0.6845 (mp0) cc_final: 0.6403 (mp0) REVERT: J 157 ARG cc_start: 0.8824 (ptt-90) cc_final: 0.8339 (ptt-90) REVERT: J 170 PHE cc_start: 0.8250 (t80) cc_final: 0.7240 (t80) REVERT: J 174 LEU cc_start: 0.8958 (mm) cc_final: 0.8713 (pp) REVERT: J 201 PHE cc_start: 0.8742 (m-80) cc_final: 0.8427 (m-10) REVERT: J 205 PHE cc_start: 0.8930 (m-80) cc_final: 0.8469 (m-80) REVERT: J 217 PHE cc_start: 0.9113 (t80) cc_final: 0.8291 (t80) REVERT: J 221 PHE cc_start: 0.8879 (t80) cc_final: 0.8304 (t80) REVERT: J 223 TYR cc_start: 0.8700 (m-80) cc_final: 0.8177 (m-80) REVERT: J 247 PHE cc_start: 0.9104 (m-80) cc_final: 0.8696 (m-10) REVERT: J 277 HIS cc_start: 0.9114 (t-90) cc_final: 0.8860 (t-90) REVERT: J 411 GLN cc_start: 0.8840 (tp-100) cc_final: 0.8481 (pt0) REVERT: J 436 TYR cc_start: 0.6888 (m-10) cc_final: 0.6507 (m-80) REVERT: J 590 ARG cc_start: 0.6762 (mmp80) cc_final: 0.4472 (ttm110) outliers start: 1 outliers final: 0 residues processed: 1048 average time/residue: 0.5243 time to fit residues: 899.2265 Evaluate side-chains 867 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 867 time to evaluate : 5.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 339 optimal weight: 0.8980 chunk 219 optimal weight: 10.0000 chunk 328 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 349 optimal weight: 5.9990 chunk 374 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 431 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 HIS ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 594 ASN H 745 HIS ** I 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 HIS ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 ASN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 42867 Z= 0.211 Angle : 0.597 10.712 58454 Z= 0.309 Chirality : 0.045 0.246 6899 Planarity : 0.004 0.070 7709 Dihedral : 4.536 24.054 6111 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.44 (0.11), residues: 5708 helix: 0.38 (0.13), residues: 1606 sheet: -0.16 (0.16), residues: 1054 loop : -0.65 (0.11), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 271 HIS 0.005 0.001 HIS E 336 PHE 0.027 0.001 PHE A 531 TYR 0.038 0.001 TYR I 167 ARG 0.006 0.001 ARG H 391 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 982 time to evaluate : 5.323 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8185 (tm-30) REVERT: A 200 ARG cc_start: 0.7499 (mpt180) cc_final: 0.7126 (mpt-90) REVERT: A 324 PHE cc_start: 0.8233 (p90) cc_final: 0.7781 (p90) REVERT: A 391 LEU cc_start: 0.9204 (mm) cc_final: 0.8959 (mm) REVERT: A 415 ASN cc_start: 0.8679 (m110) cc_final: 0.8448 (m110) REVERT: A 436 TYR cc_start: 0.9085 (t80) cc_final: 0.8556 (t80) REVERT: A 453 ASP cc_start: 0.8873 (p0) cc_final: 0.8200 (p0) REVERT: A 456 TYR cc_start: 0.8519 (m-10) cc_final: 0.8314 (m-10) REVERT: A 465 GLU cc_start: 0.8568 (mp0) cc_final: 0.8367 (pm20) REVERT: A 490 ARG cc_start: 0.8671 (ptm160) cc_final: 0.8282 (ptm-80) REVERT: A 493 PHE cc_start: 0.8592 (t80) cc_final: 0.8309 (t80) REVERT: A 514 LEU cc_start: 0.9415 (tt) cc_final: 0.9044 (tt) REVERT: A 525 GLU cc_start: 0.9294 (mp0) cc_final: 0.9027 (mp0) REVERT: A 551 ASP cc_start: 0.8388 (t0) cc_final: 0.7443 (p0) REVERT: A 552 PHE cc_start: 0.9217 (m-80) cc_final: 0.8722 (m-80) REVERT: A 598 TYR cc_start: 0.6683 (m-10) cc_final: 0.6136 (m-10) REVERT: A 631 ILE cc_start: 0.9022 (mp) cc_final: 0.8512 (tp) REVERT: A 635 ILE cc_start: 0.9613 (mm) cc_final: 0.9403 (mm) REVERT: A 727 PHE cc_start: 0.9065 (t80) cc_final: 0.8625 (t80) REVERT: B 185 ASP cc_start: 0.8574 (p0) cc_final: 0.8282 (p0) REVERT: B 192 TYR cc_start: 0.8867 (p90) cc_final: 0.8050 (p90) REVERT: B 225 LYS cc_start: 0.9307 (ttpt) cc_final: 0.8893 (ttpt) REVERT: B 227 SER cc_start: 0.9116 (p) cc_final: 0.8883 (m) REVERT: B 244 ASP cc_start: 0.8610 (t70) cc_final: 0.7998 (t70) REVERT: B 246 ASN cc_start: 0.9128 (m110) cc_final: 0.8690 (m110) REVERT: B 328 ASN cc_start: 0.7381 (t0) cc_final: 0.6956 (t0) REVERT: B 378 LEU cc_start: 0.9139 (tp) cc_final: 0.8578 (tt) REVERT: B 410 TYR cc_start: 0.8879 (m-10) cc_final: 0.8639 (m-10) REVERT: B 470 ARG cc_start: 0.8264 (ptp90) cc_final: 0.7124 (ttp80) REVERT: B 515 GLU cc_start: 0.7954 (tp30) cc_final: 0.7261 (tm-30) REVERT: B 551 ASP cc_start: 0.7784 (p0) cc_final: 0.7511 (p0) REVERT: B 561 ASN cc_start: 0.9062 (m110) cc_final: 0.8666 (m110) REVERT: B 565 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8738 (mt0) REVERT: B 727 PHE cc_start: 0.8565 (t80) cc_final: 0.8290 (t80) REVERT: C 195 ASP cc_start: 0.7826 (t0) cc_final: 0.7411 (t0) REVERT: C 243 ILE cc_start: 0.9414 (tp) cc_final: 0.8824 (tp) REVERT: C 244 ASP cc_start: 0.8749 (t0) cc_final: 0.8317 (t70) REVERT: C 328 ASN cc_start: 0.7424 (p0) cc_final: 0.6922 (p0) REVERT: C 336 HIS cc_start: 0.9040 (p-80) cc_final: 0.8444 (p-80) REVERT: C 343 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7358 (mp0) REVERT: C 408 ASN cc_start: 0.9292 (t0) cc_final: 0.9073 (t0) REVERT: C 434 MET cc_start: 0.9005 (ppp) cc_final: 0.8804 (ppp) REVERT: C 479 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8082 (mt-10) REVERT: C 497 ASP cc_start: 0.8214 (p0) cc_final: 0.7948 (p0) REVERT: C 512 ASP cc_start: 0.8646 (t0) cc_final: 0.7976 (t0) REVERT: C 528 LYS cc_start: 0.9131 (ttmm) cc_final: 0.8614 (mmtt) REVERT: C 550 PHE cc_start: 0.9335 (m-80) cc_final: 0.8848 (m-80) REVERT: C 552 PHE cc_start: 0.8747 (m-80) cc_final: 0.8385 (m-80) REVERT: C 575 TYR cc_start: 0.7208 (m-80) cc_final: 0.6637 (m-80) REVERT: C 590 LEU cc_start: 0.9322 (tt) cc_final: 0.9033 (tt) REVERT: C 596 PHE cc_start: 0.9051 (m-80) cc_final: 0.8475 (m-80) REVERT: C 727 PHE cc_start: 0.8021 (t80) cc_final: 0.7761 (t80) REVERT: D 192 TYR cc_start: 0.9168 (p90) cc_final: 0.8728 (p90) REVERT: D 195 ASP cc_start: 0.8204 (t0) cc_final: 0.7994 (t70) REVERT: D 299 HIS cc_start: 0.8732 (t-90) cc_final: 0.8470 (t-90) REVERT: D 408 ASN cc_start: 0.9209 (t0) cc_final: 0.8921 (t0) REVERT: D 411 TYR cc_start: 0.8040 (t80) cc_final: 0.7819 (t80) REVERT: D 441 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8927 (pt0) REVERT: D 447 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7633 (tm-30) REVERT: D 456 TYR cc_start: 0.9044 (m-80) cc_final: 0.8762 (m-80) REVERT: D 468 ARG cc_start: 0.8897 (ttm110) cc_final: 0.8580 (ttm110) REVERT: D 525 GLU cc_start: 0.8923 (mp0) cc_final: 0.8601 (mp0) REVERT: D 554 PHE cc_start: 0.8856 (m-80) cc_final: 0.8433 (m-80) REVERT: D 565 GLN cc_start: 0.9428 (mm-40) cc_final: 0.9176 (mt0) REVERT: D 617 ARG cc_start: 0.8975 (ptp-110) cc_final: 0.8671 (ptp-110) REVERT: D 635 ILE cc_start: 0.9466 (tt) cc_final: 0.9102 (pt) REVERT: D 703 LYS cc_start: 0.9558 (mppt) cc_final: 0.9291 (mmtm) REVERT: E 202 PHE cc_start: 0.8445 (t80) cc_final: 0.8140 (t80) REVERT: E 216 LEU cc_start: 0.9222 (mt) cc_final: 0.8994 (mt) REVERT: E 299 HIS cc_start: 0.8624 (t70) cc_final: 0.8390 (t-90) REVERT: E 385 LEU cc_start: 0.7696 (pt) cc_final: 0.7210 (pt) REVERT: E 389 GLN cc_start: 0.9028 (mp10) cc_final: 0.8692 (mp10) REVERT: E 411 TYR cc_start: 0.8590 (t80) cc_final: 0.7956 (t80) REVERT: E 436 TYR cc_start: 0.8710 (t80) cc_final: 0.8100 (t80) REVERT: E 509 ASN cc_start: 0.9255 (t0) cc_final: 0.8945 (t0) REVERT: E 512 ASP cc_start: 0.8003 (t0) cc_final: 0.7643 (t0) REVERT: E 553 ASN cc_start: 0.8720 (m-40) cc_final: 0.8120 (m-40) REVERT: E 616 HIS cc_start: 0.8935 (m90) cc_final: 0.8534 (m90) REVERT: F 176 PRO cc_start: 0.8750 (Cg_exo) cc_final: 0.8487 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8352 (tm-30) REVERT: F 195 ASP cc_start: 0.8919 (t0) cc_final: 0.8533 (t0) REVERT: F 223 PRO cc_start: 0.9387 (Cg_endo) cc_final: 0.9063 (Cg_exo) REVERT: F 226 TRP cc_start: 0.9388 (t60) cc_final: 0.9131 (t-100) REVERT: F 236 PHE cc_start: 0.8915 (t80) cc_final: 0.8698 (t80) REVERT: F 242 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7450 (mtp180) REVERT: F 265 ASP cc_start: 0.8863 (t0) cc_final: 0.8302 (p0) REVERT: F 326 ASN cc_start: 0.7833 (m-40) cc_final: 0.6432 (m-40) REVERT: F 366 TYR cc_start: 0.8738 (m-10) cc_final: 0.8382 (m-10) REVERT: F 439 PHE cc_start: 0.9574 (t80) cc_final: 0.9226 (t80) REVERT: F 453 ASP cc_start: 0.8829 (p0) cc_final: 0.8496 (p0) REVERT: F 486 GLU cc_start: 0.8209 (mp0) cc_final: 0.7907 (mp0) REVERT: F 490 ARG cc_start: 0.7981 (ttt180) cc_final: 0.7537 (ttp80) REVERT: F 501 VAL cc_start: 0.9171 (t) cc_final: 0.8922 (p) REVERT: F 512 ASP cc_start: 0.7707 (m-30) cc_final: 0.7453 (m-30) REVERT: F 523 LEU cc_start: 0.9406 (tp) cc_final: 0.9126 (tp) REVERT: F 551 ASP cc_start: 0.7480 (t0) cc_final: 0.6852 (p0) REVERT: F 590 LEU cc_start: 0.7874 (mt) cc_final: 0.7670 (mt) REVERT: F 602 ASN cc_start: 0.9299 (m-40) cc_final: 0.8722 (m110) REVERT: G 246 ASN cc_start: 0.8217 (t0) cc_final: 0.7964 (t0) REVERT: G 266 MET cc_start: 0.8732 (tpp) cc_final: 0.8429 (tpp) REVERT: G 328 ASN cc_start: 0.7758 (t0) cc_final: 0.7552 (t0) REVERT: G 334 ILE cc_start: 0.8633 (mp) cc_final: 0.8112 (tp) REVERT: G 365 ARG cc_start: 0.7677 (mtt-85) cc_final: 0.7237 (mmt180) REVERT: G 439 PHE cc_start: 0.9282 (t80) cc_final: 0.9073 (t80) REVERT: G 448 LEU cc_start: 0.9540 (mm) cc_final: 0.9266 (mm) REVERT: G 456 TYR cc_start: 0.9051 (m-10) cc_final: 0.8777 (m-10) REVERT: G 479 GLU cc_start: 0.8878 (mp0) cc_final: 0.8631 (mp0) REVERT: G 512 ASP cc_start: 0.8499 (t0) cc_final: 0.8147 (t0) REVERT: G 550 PHE cc_start: 0.8066 (m-80) cc_final: 0.7406 (m-80) REVERT: G 551 ASP cc_start: 0.8940 (t0) cc_final: 0.7666 (p0) REVERT: G 552 PHE cc_start: 0.8926 (m-80) cc_final: 0.8657 (m-80) REVERT: G 561 ASN cc_start: 0.9524 (t0) cc_final: 0.9266 (t0) REVERT: G 569 LEU cc_start: 0.9261 (mt) cc_final: 0.9034 (mt) REVERT: G 583 LEU cc_start: 0.9188 (mt) cc_final: 0.8906 (mm) REVERT: G 596 PHE cc_start: 0.9189 (m-80) cc_final: 0.8965 (m-80) REVERT: G 727 PHE cc_start: 0.8204 (t80) cc_final: 0.7630 (t80) REVERT: H 145 LEU cc_start: 0.9190 (mt) cc_final: 0.8859 (mt) REVERT: H 158 ASP cc_start: 0.9366 (t0) cc_final: 0.9092 (m-30) REVERT: H 170 PHE cc_start: 0.9316 (t80) cc_final: 0.8646 (t80) REVERT: H 174 LEU cc_start: 0.9627 (mt) cc_final: 0.9367 (mt) REVERT: H 200 ASP cc_start: 0.9324 (p0) cc_final: 0.9051 (p0) REVERT: H 217 PHE cc_start: 0.8805 (t80) cc_final: 0.8330 (t80) REVERT: H 234 GLN cc_start: 0.8950 (mt0) cc_final: 0.8379 (mp10) REVERT: H 281 TRP cc_start: 0.8741 (t60) cc_final: 0.7922 (t60) REVERT: H 390 GLN cc_start: 0.8759 (mp10) cc_final: 0.8551 (mp10) REVERT: H 438 TYR cc_start: 0.8488 (m-80) cc_final: 0.8194 (m-80) REVERT: H 441 MET cc_start: 0.8096 (tmm) cc_final: 0.7613 (tmm) REVERT: H 470 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8179 (mp0) REVERT: H 484 MET cc_start: 0.8223 (mpp) cc_final: 0.7851 (mpp) REVERT: H 486 VAL cc_start: 0.8837 (m) cc_final: 0.8583 (p) REVERT: H 499 LEU cc_start: 0.8762 (mp) cc_final: 0.7556 (mp) REVERT: H 521 LEU cc_start: 0.9489 (mm) cc_final: 0.9041 (mm) REVERT: H 568 GLN cc_start: 0.8510 (pp30) cc_final: 0.6215 (pp30) REVERT: H 605 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8755 (pt0) REVERT: H 611 GLN cc_start: 0.8367 (tp40) cc_final: 0.8110 (tp40) REVERT: H 690 HIS cc_start: 0.8006 (m-70) cc_final: 0.7684 (m170) REVERT: H 736 PHE cc_start: 0.8890 (t80) cc_final: 0.8436 (t80) REVERT: H 737 PHE cc_start: 0.9107 (m-80) cc_final: 0.8487 (m-80) REVERT: H 741 PHE cc_start: 0.9614 (t80) cc_final: 0.9379 (t80) REVERT: I 149 TYR cc_start: 0.9040 (t80) cc_final: 0.8784 (t80) REVERT: I 154 ILE cc_start: 0.9201 (mm) cc_final: 0.8869 (mm) REVERT: I 158 ASP cc_start: 0.8840 (m-30) cc_final: 0.8462 (m-30) REVERT: I 205 PHE cc_start: 0.8327 (m-80) cc_final: 0.7915 (m-80) REVERT: I 230 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.7964 (ttm170) REVERT: I 244 MET cc_start: 0.9516 (tpt) cc_final: 0.9239 (tpt) REVERT: I 259 LEU cc_start: 0.9228 (pp) cc_final: 0.8930 (mt) REVERT: I 264 MET cc_start: 0.8391 (pmm) cc_final: 0.7648 (pmm) REVERT: I 268 TYR cc_start: 0.8942 (m-10) cc_final: 0.8723 (m-80) REVERT: I 281 TRP cc_start: 0.8497 (t60) cc_final: 0.8166 (t60) REVERT: I 440 ASN cc_start: 0.7611 (m-40) cc_final: 0.7286 (m-40) REVERT: I 441 MET cc_start: 0.6217 (tmm) cc_final: 0.5213 (tmm) REVERT: I 546 ASP cc_start: 0.8462 (p0) cc_final: 0.7403 (p0) REVERT: I 597 GLU cc_start: 0.6840 (mp0) cc_final: 0.6444 (mp0) REVERT: J 170 PHE cc_start: 0.8265 (t80) cc_final: 0.7209 (t80) REVERT: J 174 LEU cc_start: 0.8955 (mm) cc_final: 0.8727 (pp) REVERT: J 201 PHE cc_start: 0.8835 (m-80) cc_final: 0.8450 (m-10) REVERT: J 205 PHE cc_start: 0.8915 (m-80) cc_final: 0.8453 (m-80) REVERT: J 217 PHE cc_start: 0.9104 (t80) cc_final: 0.8287 (t80) REVERT: J 221 PHE cc_start: 0.8810 (t80) cc_final: 0.8088 (t80) REVERT: J 241 PHE cc_start: 0.9037 (t80) cc_final: 0.8833 (t80) REVERT: J 247 PHE cc_start: 0.9089 (m-80) cc_final: 0.8703 (m-10) REVERT: J 277 HIS cc_start: 0.9093 (t-90) cc_final: 0.8836 (t-90) REVERT: J 411 GLN cc_start: 0.8800 (tp-100) cc_final: 0.8453 (pt0) REVERT: J 436 TYR cc_start: 0.6801 (m-10) cc_final: 0.6465 (m-80) outliers start: 0 outliers final: 0 residues processed: 982 average time/residue: 0.5759 time to fit residues: 934.8868 Evaluate side-chains 826 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 826 time to evaluate : 4.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 499 optimal weight: 9.9990 chunk 526 optimal weight: 6.9990 chunk 480 optimal weight: 9.9990 chunk 511 optimal weight: 7.9990 chunk 308 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 402 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 462 optimal weight: 40.0000 chunk 484 optimal weight: 6.9990 chunk 510 optimal weight: 4.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 561 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 HIS B 588 ASN B 616 HIS C 602 ASN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 HIS ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 GLN H 242 ASN H 440 ASN ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 594 ASN H 604 ASN ** H 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 ASN ** I 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 563 GLN ** J 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 ASN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.176 42867 Z= 0.590 Angle : 0.850 15.211 58454 Z= 0.447 Chirality : 0.049 0.231 6899 Planarity : 0.006 0.100 7709 Dihedral : 5.580 26.958 6111 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 25.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.62 % Favored : 92.36 % Rotamer: Outliers : 0.02 % Allowed : 1.38 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.99 (0.11), residues: 5708 helix: -0.01 (0.13), residues: 1608 sheet: -0.47 (0.15), residues: 1095 loop : -1.04 (0.11), residues: 3005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP H 271 HIS 0.011 0.002 HIS B 253 PHE 0.033 0.003 PHE B 550 TYR 0.047 0.003 TYR D 233 ARG 0.013 0.001 ARG C 468 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 857 time to evaluate : 5.325 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: 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: A 190 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8271 (tm-30) REVERT: A 192 TYR cc_start: 0.9102 (p90) cc_final: 0.8786 (p90) REVERT: A 200 ARG cc_start: 0.7643 (mpt180) cc_final: 0.7278 (mpt-90) REVERT: A 324 PHE cc_start: 0.8324 (p90) cc_final: 0.8032 (p90) REVERT: A 415 ASN cc_start: 0.8832 (m110) cc_final: 0.8545 (m110) REVERT: A 436 TYR cc_start: 0.9078 (t80) cc_final: 0.8818 (t80) REVERT: A 439 PHE cc_start: 0.9410 (t80) cc_final: 0.9200 (t80) REVERT: A 453 ASP cc_start: 0.8903 (p0) cc_final: 0.8278 (p0) REVERT: A 456 TYR cc_start: 0.8612 (m-10) cc_final: 0.8357 (m-10) REVERT: A 522 THR cc_start: 0.9293 (m) cc_final: 0.8882 (m) REVERT: A 525 GLU cc_start: 0.9256 (mp0) cc_final: 0.8993 (mp0) REVERT: A 561 ASN cc_start: 0.9564 (t160) cc_final: 0.9357 (t0) REVERT: A 583 LEU cc_start: 0.9383 (mm) cc_final: 0.8869 (mm) REVERT: A 614 GLU cc_start: 0.9003 (tp30) cc_final: 0.8724 (mm-30) REVERT: A 727 PHE cc_start: 0.9137 (t80) cc_final: 0.8714 (t80) REVERT: B 185 ASP cc_start: 0.8775 (p0) cc_final: 0.8538 (p0) REVERT: B 190 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8523 (tm-30) REVERT: B 192 TYR cc_start: 0.8970 (p90) cc_final: 0.8420 (p90) REVERT: B 225 LYS cc_start: 0.9445 (ttpt) cc_final: 0.9192 (tttt) REVERT: B 243 ILE cc_start: 0.9156 (tt) cc_final: 0.8508 (pt) REVERT: B 244 ASP cc_start: 0.8573 (t70) cc_final: 0.8065 (t0) REVERT: B 246 ASN cc_start: 0.9176 (m110) cc_final: 0.8836 (m110) REVERT: B 265 ASP cc_start: 0.8542 (t0) cc_final: 0.8337 (t0) REVERT: B 328 ASN cc_start: 0.7283 (t0) cc_final: 0.6887 (t0) REVERT: B 439 PHE cc_start: 0.9277 (t80) cc_final: 0.9024 (t80) REVERT: B 470 ARG cc_start: 0.8459 (ptp90) cc_final: 0.7552 (ttp80) REVERT: B 486 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8926 (tm-30) REVERT: B 501 VAL cc_start: 0.9565 (t) cc_final: 0.9333 (p) REVERT: B 504 ARG cc_start: 0.7313 (mmm-85) cc_final: 0.6952 (mmm-85) REVERT: B 515 GLU cc_start: 0.8099 (tp30) cc_final: 0.7830 (tp30) REVERT: B 561 ASN cc_start: 0.9043 (m110) cc_final: 0.8654 (m110) REVERT: B 565 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8699 (tt0) REVERT: B 584 ASN cc_start: 0.8730 (t0) cc_final: 0.8402 (t0) REVERT: B 727 PHE cc_start: 0.8408 (t80) cc_final: 0.8177 (t80) REVERT: C 233 TYR cc_start: 0.8173 (m-10) cc_final: 0.7865 (m-10) REVERT: C 336 HIS cc_start: 0.9112 (p-80) cc_final: 0.8460 (p-80) REVERT: C 343 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7540 (mp0) REVERT: C 368 ASN cc_start: 0.8952 (t0) cc_final: 0.8737 (t0) REVERT: C 408 ASN cc_start: 0.9390 (t0) cc_final: 0.9139 (t0) REVERT: C 476 ASN cc_start: 0.9257 (p0) cc_final: 0.8796 (p0) REVERT: C 497 ASP cc_start: 0.8302 (p0) cc_final: 0.7996 (p0) REVERT: C 528 LYS cc_start: 0.9238 (ttmm) cc_final: 0.8742 (mmtt) REVERT: C 552 PHE cc_start: 0.8732 (m-80) cc_final: 0.8283 (m-80) REVERT: C 575 TYR cc_start: 0.7349 (m-80) cc_final: 0.6722 (m-80) REVERT: C 590 LEU cc_start: 0.9379 (tt) cc_final: 0.9065 (tt) REVERT: C 596 PHE cc_start: 0.9226 (m-80) cc_final: 0.8620 (m-80) REVERT: C 727 PHE cc_start: 0.7880 (t80) cc_final: 0.7544 (t80) REVERT: D 192 TYR cc_start: 0.9220 (p90) cc_final: 0.8944 (p90) REVERT: D 195 ASP cc_start: 0.8247 (t0) cc_final: 0.8003 (t0) REVERT: D 224 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7726 (mm-30) REVERT: D 246 ASN cc_start: 0.9320 (m110) cc_final: 0.8854 (m110) REVERT: D 360 LEU cc_start: 0.9476 (tp) cc_final: 0.9140 (tp) REVERT: D 394 ILE cc_start: 0.9129 (mp) cc_final: 0.8920 (mp) REVERT: D 405 LEU cc_start: 0.9199 (tp) cc_final: 0.8810 (tp) REVERT: D 437 ASN cc_start: 0.9426 (m-40) cc_final: 0.9197 (m110) REVERT: D 441 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8912 (mt-10) REVERT: D 486 GLU cc_start: 0.8640 (tt0) cc_final: 0.8414 (tt0) REVERT: D 525 GLU cc_start: 0.8961 (mp0) cc_final: 0.8622 (mp0) REVERT: D 565 GLN cc_start: 0.9442 (mm-40) cc_final: 0.9064 (mt0) REVERT: D 617 ARG cc_start: 0.9034 (ptp-110) cc_final: 0.8767 (ptp-110) REVERT: D 635 ILE cc_start: 0.9406 (tt) cc_final: 0.9037 (pt) REVERT: D 703 LYS cc_start: 0.9522 (mppt) cc_final: 0.9241 (mmtm) REVERT: E 192 TYR cc_start: 0.9012 (p90) cc_final: 0.8560 (p90) REVERT: E 202 PHE cc_start: 0.8533 (t80) cc_final: 0.8180 (t80) REVERT: E 385 LEU cc_start: 0.7714 (pt) cc_final: 0.7060 (pp) REVERT: E 389 GLN cc_start: 0.9084 (mp10) cc_final: 0.8600 (mp10) REVERT: E 411 TYR cc_start: 0.8874 (t80) cc_final: 0.8479 (t80) REVERT: E 436 TYR cc_start: 0.8677 (t80) cc_final: 0.8352 (t80) REVERT: E 512 ASP cc_start: 0.8378 (t0) cc_final: 0.8103 (t0) REVERT: E 553 ASN cc_start: 0.8928 (m-40) cc_final: 0.8462 (m-40) REVERT: E 590 LEU cc_start: 0.9194 (mt) cc_final: 0.8945 (mt) REVERT: F 176 PRO cc_start: 0.8847 (Cg_exo) cc_final: 0.8619 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8303 (tm-30) REVERT: F 192 TYR cc_start: 0.8366 (p90) cc_final: 0.7779 (p90) REVERT: F 242 ARG cc_start: 0.7905 (mtp180) cc_final: 0.7072 (mtp180) REVERT: F 265 ASP cc_start: 0.8865 (t0) cc_final: 0.8335 (p0) REVERT: F 326 ASN cc_start: 0.7689 (m-40) cc_final: 0.7291 (m-40) REVERT: F 366 TYR cc_start: 0.9177 (m-10) cc_final: 0.8831 (m-10) REVERT: F 439 PHE cc_start: 0.9547 (t80) cc_final: 0.9240 (t80) REVERT: F 441 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8846 (mm-30) REVERT: F 453 ASP cc_start: 0.8856 (p0) cc_final: 0.8515 (p0) REVERT: F 462 TYR cc_start: 0.7714 (t80) cc_final: 0.6785 (t80) REVERT: F 479 GLU cc_start: 0.9358 (mp0) cc_final: 0.9075 (mp0) REVERT: F 486 GLU cc_start: 0.8447 (mp0) cc_final: 0.8220 (mp0) REVERT: F 497 ASP cc_start: 0.8805 (p0) cc_final: 0.8495 (p0) REVERT: F 501 VAL cc_start: 0.9223 (t) cc_final: 0.9001 (p) REVERT: F 512 ASP cc_start: 0.7813 (m-30) cc_final: 0.7534 (m-30) REVERT: F 521 MET cc_start: 0.8221 (pmm) cc_final: 0.7788 (pmm) REVERT: F 523 LEU cc_start: 0.9462 (tp) cc_final: 0.9220 (tp) REVERT: F 528 LYS cc_start: 0.9429 (ttmm) cc_final: 0.8939 (mmmt) REVERT: F 551 ASP cc_start: 0.7469 (t0) cc_final: 0.6808 (p0) REVERT: G 266 MET cc_start: 0.8649 (tpp) cc_final: 0.8361 (tpp) REVERT: G 299 HIS cc_start: 0.8654 (t-90) cc_final: 0.8305 (t-90) REVERT: G 334 ILE cc_start: 0.8912 (mp) cc_final: 0.8326 (tp) REVERT: G 365 ARG cc_start: 0.7707 (mtt-85) cc_final: 0.7494 (mtt-85) REVERT: G 405 LEU cc_start: 0.9201 (mp) cc_final: 0.8891 (mp) REVERT: G 439 PHE cc_start: 0.9319 (t80) cc_final: 0.9064 (t80) REVERT: G 448 LEU cc_start: 0.9523 (mm) cc_final: 0.9268 (mm) REVERT: G 512 ASP cc_start: 0.8486 (t0) cc_final: 0.8220 (t0) REVERT: G 551 ASP cc_start: 0.9013 (t0) cc_final: 0.7807 (p0) REVERT: G 552 PHE cc_start: 0.8919 (m-80) cc_final: 0.8648 (m-80) REVERT: G 638 ILE cc_start: 0.9216 (pt) cc_final: 0.8345 (mm) REVERT: G 727 PHE cc_start: 0.8092 (t80) cc_final: 0.7570 (t80) REVERT: H 125 TYR cc_start: 0.8860 (t80) cc_final: 0.8646 (t80) REVERT: H 145 LEU cc_start: 0.9270 (mt) cc_final: 0.8992 (mt) REVERT: H 170 PHE cc_start: 0.9449 (t80) cc_final: 0.8878 (t80) REVERT: H 174 LEU cc_start: 0.9654 (mt) cc_final: 0.9442 (mt) REVERT: H 200 ASP cc_start: 0.9415 (p0) cc_final: 0.9150 (p0) REVERT: H 217 PHE cc_start: 0.8959 (t80) cc_final: 0.8693 (t80) REVERT: H 244 MET cc_start: 0.9227 (tpt) cc_final: 0.8499 (tpt) REVERT: H 281 TRP cc_start: 0.8775 (t60) cc_final: 0.8125 (t60) REVERT: H 438 TYR cc_start: 0.8723 (m-80) cc_final: 0.8332 (m-80) REVERT: H 484 MET cc_start: 0.8151 (mpp) cc_final: 0.7932 (mpp) REVERT: H 499 LEU cc_start: 0.8758 (mp) cc_final: 0.7921 (mp) REVERT: H 521 LEU cc_start: 0.9557 (mm) cc_final: 0.9172 (mm) REVERT: H 568 GLN cc_start: 0.8622 (pp30) cc_final: 0.6775 (pt0) REVERT: H 591 TYR cc_start: 0.8573 (t80) cc_final: 0.8351 (t80) REVERT: H 605 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8959 (mt-10) REVERT: H 611 GLN cc_start: 0.8308 (tp40) cc_final: 0.7967 (tp-100) REVERT: H 736 PHE cc_start: 0.8890 (t80) cc_final: 0.8559 (t80) REVERT: H 737 PHE cc_start: 0.9186 (m-80) cc_final: 0.8818 (m-80) REVERT: H 744 MET cc_start: 0.9118 (ptt) cc_final: 0.8914 (ptt) REVERT: H 745 HIS cc_start: 0.8885 (m-70) cc_final: 0.8615 (m90) REVERT: I 35 HIS cc_start: 0.7740 (m90) cc_final: 0.7531 (m90) REVERT: I 149 TYR cc_start: 0.9274 (t80) cc_final: 0.8928 (t80) REVERT: I 157 ARG cc_start: 0.8655 (ttp80) cc_final: 0.8141 (ttp80) REVERT: I 158 ASP cc_start: 0.9033 (m-30) cc_final: 0.8681 (m-30) REVERT: I 205 PHE cc_start: 0.8481 (m-80) cc_final: 0.8119 (m-10) REVERT: I 230 ARG cc_start: 0.8714 (ttm-80) cc_final: 0.7994 (tpp80) REVERT: I 244 MET cc_start: 0.9515 (tpt) cc_final: 0.9136 (tpt) REVERT: I 259 LEU cc_start: 0.9296 (pp) cc_final: 0.9041 (mt) REVERT: I 264 MET cc_start: 0.8248 (pmm) cc_final: 0.7526 (pmm) REVERT: I 268 TYR cc_start: 0.8936 (m-10) cc_final: 0.8707 (m-80) REVERT: I 281 TRP cc_start: 0.8490 (t60) cc_final: 0.8035 (t60) REVERT: I 533 GLN cc_start: 0.7195 (pm20) cc_final: 0.6954 (pm20) REVERT: J 170 PHE cc_start: 0.8371 (t80) cc_final: 0.7422 (t80) REVERT: J 201 PHE cc_start: 0.8847 (m-80) cc_final: 0.8457 (m-10) REVERT: J 205 PHE cc_start: 0.8928 (m-80) cc_final: 0.8503 (m-80) REVERT: J 221 PHE cc_start: 0.8773 (t80) cc_final: 0.8229 (t80) REVERT: J 247 PHE cc_start: 0.9111 (m-80) cc_final: 0.8676 (m-10) REVERT: J 277 HIS cc_start: 0.9107 (t-90) cc_final: 0.8864 (t-90) REVERT: J 411 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8468 (pt0) REVERT: J 436 TYR cc_start: 0.6750 (m-10) cc_final: 0.6445 (m-80) outliers start: 1 outliers final: 0 residues processed: 857 average time/residue: 0.5493 time to fit residues: 768.3663 Evaluate side-chains 737 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 737 time to evaluate : 4.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 336 optimal weight: 0.9990 chunk 541 optimal weight: 6.9990 chunk 330 optimal weight: 0.9980 chunk 256 optimal weight: 30.0000 chunk 376 optimal weight: 2.9990 chunk 567 optimal weight: 7.9990 chunk 522 optimal weight: 0.9980 chunk 452 optimal weight: 0.9980 chunk 46 optimal weight: 30.0000 chunk 349 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 HIS A 630 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN D 263 HIS ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 ASN H 594 ASN H 620 ASN ** H 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 HIS ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 ASN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 42867 Z= 0.206 Angle : 0.630 11.815 58454 Z= 0.329 Chirality : 0.046 0.242 6899 Planarity : 0.004 0.077 7709 Dihedral : 4.892 28.264 6111 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.11), residues: 5708 helix: 0.22 (0.13), residues: 1601 sheet: -0.25 (0.16), residues: 1024 loop : -0.83 (0.11), residues: 3083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 271 HIS 0.008 0.001 HIS E 336 PHE 0.030 0.001 PHE B 552 TYR 0.052 0.002 TYR I 167 ARG 0.014 0.001 ARG C 468 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11416 Ramachandran restraints generated. 5708 Oldfield, 0 Emsley, 5708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 969 time to evaluate : 5.299 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8192 (tm-30) REVERT: A 192 TYR cc_start: 0.8900 (p90) cc_final: 0.8690 (p90) REVERT: A 200 ARG cc_start: 0.7608 (mpt180) cc_final: 0.7181 (mpt-90) REVERT: A 366 TYR cc_start: 0.9211 (m-80) cc_final: 0.8999 (m-10) REVERT: A 415 ASN cc_start: 0.8748 (m110) cc_final: 0.8445 (m110) REVERT: A 436 TYR cc_start: 0.9044 (t80) cc_final: 0.8500 (t80) REVERT: A 439 PHE cc_start: 0.9424 (t80) cc_final: 0.9211 (t80) REVERT: A 453 ASP cc_start: 0.8898 (p0) cc_final: 0.8262 (p0) REVERT: A 525 GLU cc_start: 0.9234 (mp0) cc_final: 0.8976 (mp0) REVERT: A 595 ARG cc_start: 0.8566 (mmp80) cc_final: 0.8264 (mmp80) REVERT: A 727 PHE cc_start: 0.9079 (t80) cc_final: 0.8655 (t80) REVERT: B 185 ASP cc_start: 0.8535 (p0) cc_final: 0.8265 (p0) REVERT: B 190 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8416 (tm-30) REVERT: B 192 TYR cc_start: 0.8887 (p90) cc_final: 0.8155 (p90) REVERT: B 225 LYS cc_start: 0.9385 (ttpt) cc_final: 0.8988 (ttpt) REVERT: B 227 SER cc_start: 0.9258 (p) cc_final: 0.9004 (m) REVERT: B 244 ASP cc_start: 0.8363 (t70) cc_final: 0.7871 (t0) REVERT: B 246 ASN cc_start: 0.9014 (m110) cc_final: 0.8566 (m110) REVERT: B 265 ASP cc_start: 0.8490 (t0) cc_final: 0.8225 (t0) REVERT: B 328 ASN cc_start: 0.7560 (t0) cc_final: 0.7083 (t0) REVERT: B 439 PHE cc_start: 0.9179 (t80) cc_final: 0.8971 (t80) REVERT: B 468 ARG cc_start: 0.8142 (mmm-85) cc_final: 0.7894 (mmm-85) REVERT: B 470 ARG cc_start: 0.8197 (ptp90) cc_final: 0.6909 (ttp80) REVERT: B 486 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8819 (tm-30) REVERT: B 501 VAL cc_start: 0.9501 (t) cc_final: 0.9290 (p) REVERT: B 561 ASN cc_start: 0.9041 (m110) cc_final: 0.8602 (m110) REVERT: B 565 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8635 (tt0) REVERT: B 584 ASN cc_start: 0.8444 (t0) cc_final: 0.8200 (t0) REVERT: B 727 PHE cc_start: 0.8414 (t80) cc_final: 0.8185 (t80) REVERT: C 185 ASP cc_start: 0.8759 (p0) cc_final: 0.8429 (p0) REVERT: C 195 ASP cc_start: 0.7830 (t0) cc_final: 0.7405 (t0) REVERT: C 244 ASP cc_start: 0.8850 (t0) cc_final: 0.8142 (t70) REVERT: C 328 ASN cc_start: 0.7494 (p0) cc_final: 0.6815 (p0) REVERT: C 336 HIS cc_start: 0.9085 (p-80) cc_final: 0.8359 (p-80) REVERT: C 343 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7420 (mp0) REVERT: C 408 ASN cc_start: 0.9289 (t0) cc_final: 0.9084 (t0) REVERT: C 434 MET cc_start: 0.8608 (ppp) cc_final: 0.8373 (ppp) REVERT: C 479 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8226 (mt-10) REVERT: C 497 ASP cc_start: 0.8259 (p0) cc_final: 0.7979 (p0) REVERT: C 512 ASP cc_start: 0.8512 (t0) cc_final: 0.7841 (t0) REVERT: C 528 LYS cc_start: 0.9179 (ttmm) cc_final: 0.8655 (mmtt) REVERT: C 552 PHE cc_start: 0.8709 (m-80) cc_final: 0.8281 (m-80) REVERT: C 575 TYR cc_start: 0.7160 (m-80) cc_final: 0.6609 (m-80) REVERT: C 590 LEU cc_start: 0.9335 (tt) cc_final: 0.9040 (tt) REVERT: C 596 PHE cc_start: 0.9213 (m-80) cc_final: 0.8808 (m-10) REVERT: C 727 PHE cc_start: 0.7996 (t80) cc_final: 0.7747 (t80) REVERT: D 365 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7366 (tpp-160) REVERT: D 408 ASN cc_start: 0.9284 (t0) cc_final: 0.8962 (t0) REVERT: D 411 TYR cc_start: 0.8095 (t80) cc_final: 0.7870 (t80) REVERT: D 437 ASN cc_start: 0.9425 (m-40) cc_final: 0.9186 (m110) REVERT: D 441 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8889 (mt-10) REVERT: D 483 GLN cc_start: 0.8562 (mp10) cc_final: 0.8184 (mp10) REVERT: D 525 GLU cc_start: 0.8940 (mp0) cc_final: 0.8632 (mp0) REVERT: D 565 GLN cc_start: 0.9437 (mm-40) cc_final: 0.9107 (mt0) REVERT: D 579 ASP cc_start: 0.9255 (p0) cc_final: 0.8911 (p0) REVERT: D 617 ARG cc_start: 0.9000 (ptp-110) cc_final: 0.8737 (ptp-110) REVERT: D 635 ILE cc_start: 0.9446 (tt) cc_final: 0.9116 (pt) REVERT: D 703 LYS cc_start: 0.9547 (mppt) cc_final: 0.9277 (mmtm) REVERT: E 202 PHE cc_start: 0.8543 (t80) cc_final: 0.8219 (t80) REVERT: E 292 ASN cc_start: 0.8543 (p0) cc_final: 0.8269 (t0) REVERT: E 299 HIS cc_start: 0.8706 (t70) cc_final: 0.8192 (t-90) REVERT: E 385 LEU cc_start: 0.7652 (pt) cc_final: 0.7005 (pp) REVERT: E 389 GLN cc_start: 0.9076 (mp10) cc_final: 0.8557 (mp10) REVERT: E 411 TYR cc_start: 0.8619 (t80) cc_final: 0.8117 (t80) REVERT: E 436 TYR cc_start: 0.8672 (t80) cc_final: 0.8149 (t80) REVERT: E 470 ARG cc_start: 0.8474 (tmm160) cc_final: 0.8251 (tmm-80) REVERT: E 512 ASP cc_start: 0.8026 (t0) cc_final: 0.6082 (t0) REVERT: E 553 ASN cc_start: 0.8731 (m-40) cc_final: 0.8315 (m-40) REVERT: F 176 PRO cc_start: 0.8777 (Cg_exo) cc_final: 0.8482 (Cg_endo) REVERT: F 190 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8391 (tm-30) REVERT: F 223 PRO cc_start: 0.9403 (Cg_endo) cc_final: 0.9004 (Cg_exo) REVERT: F 226 TRP cc_start: 0.9405 (t60) cc_final: 0.9172 (t-100) REVERT: F 236 PHE cc_start: 0.8918 (t80) cc_final: 0.8711 (t80) REVERT: F 242 ARG cc_start: 0.7938 (mtp180) cc_final: 0.7071 (mtp180) REVERT: F 245 LYS cc_start: 0.9242 (mmmt) cc_final: 0.8857 (mmmm) REVERT: F 265 ASP cc_start: 0.8811 (t0) cc_final: 0.8295 (p0) REVERT: F 326 ASN cc_start: 0.7702 (m-40) cc_final: 0.6230 (m-40) REVERT: F 366 TYR cc_start: 0.8699 (m-10) cc_final: 0.8400 (m-10) REVERT: F 436 TYR cc_start: 0.9108 (t80) cc_final: 0.8827 (t80) REVERT: F 439 PHE cc_start: 0.9526 (t80) cc_final: 0.9187 (t80) REVERT: F 453 ASP cc_start: 0.8817 (p0) cc_final: 0.8508 (p0) REVERT: F 462 TYR cc_start: 0.7701 (t80) cc_final: 0.6708 (t80) REVERT: F 480 VAL cc_start: 0.8461 (t) cc_final: 0.8047 (m) REVERT: F 490 ARG cc_start: 0.7884 (ttt180) cc_final: 0.7276 (ttp80) REVERT: F 501 VAL cc_start: 0.9097 (t) cc_final: 0.8826 (p) REVERT: F 512 ASP cc_start: 0.7678 (m-30) cc_final: 0.7313 (m-30) REVERT: F 521 MET cc_start: 0.7749 (pmm) cc_final: 0.7119 (pmm) REVERT: F 523 LEU cc_start: 0.9387 (tp) cc_final: 0.9114 (tp) REVERT: F 551 ASP cc_start: 0.7448 (t0) cc_final: 0.6763 (p0) REVERT: G 235 ASP cc_start: 0.8499 (m-30) cc_final: 0.8268 (m-30) REVERT: G 246 ASN cc_start: 0.8489 (t0) cc_final: 0.8250 (t0) REVERT: G 266 MET cc_start: 0.8731 (tpp) cc_final: 0.8340 (tpp) REVERT: G 299 HIS cc_start: 0.8709 (t-90) cc_final: 0.8414 (t-90) REVERT: G 325 SER cc_start: 0.8374 (t) cc_final: 0.8165 (p) REVERT: G 334 ILE cc_start: 0.8759 (mp) cc_final: 0.8358 (tp) REVERT: G 365 ARG cc_start: 0.7686 (mtt-85) cc_final: 0.7481 (mmt180) REVERT: G 405 LEU cc_start: 0.9168 (mp) cc_final: 0.8819 (mp) REVERT: G 439 PHE cc_start: 0.9295 (t80) cc_final: 0.8982 (t80) REVERT: G 440 LEU cc_start: 0.9150 (mt) cc_final: 0.8861 (mt) REVERT: G 448 LEU cc_start: 0.9539 (mm) cc_final: 0.9241 (mm) REVERT: G 456 TYR cc_start: 0.9021 (m-10) cc_final: 0.8725 (m-10) REVERT: G 479 GLU cc_start: 0.8890 (mp0) cc_final: 0.8575 (mp0) REVERT: G 512 ASP cc_start: 0.8431 (t0) cc_final: 0.6893 (t0) REVERT: G 515 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8147 (mm-30) REVERT: G 550 PHE cc_start: 0.8111 (m-80) cc_final: 0.7481 (m-80) REVERT: G 551 ASP cc_start: 0.8951 (t0) cc_final: 0.7824 (p0) REVERT: G 552 PHE cc_start: 0.8896 (m-80) cc_final: 0.8645 (m-80) REVERT: G 561 ASN cc_start: 0.9527 (t0) cc_final: 0.9325 (t0) REVERT: G 583 LEU cc_start: 0.9252 (mt) cc_final: 0.8960 (mm) REVERT: G 596 PHE cc_start: 0.9244 (m-80) cc_final: 0.9028 (m-80) REVERT: G 727 PHE cc_start: 0.8113 (t80) cc_final: 0.7590 (t80) REVERT: H 145 LEU cc_start: 0.9182 (mt) cc_final: 0.8862 (mt) REVERT: H 158 ASP cc_start: 0.9283 (t70) cc_final: 0.9050 (t0) REVERT: H 170 PHE cc_start: 0.9315 (t80) cc_final: 0.8559 (t80) REVERT: H 174 LEU cc_start: 0.9600 (mt) cc_final: 0.9325 (mt) REVERT: H 200 ASP cc_start: 0.9383 (p0) cc_final: 0.9087 (p0) REVERT: H 217 PHE cc_start: 0.8789 (t80) cc_final: 0.8265 (t80) REVERT: H 281 TRP cc_start: 0.8780 (t60) cc_final: 0.7944 (t60) REVERT: H 390 GLN cc_start: 0.8831 (mp10) cc_final: 0.8602 (mp10) REVERT: H 441 MET cc_start: 0.8098 (tmm) cc_final: 0.7785 (tmm) REVERT: H 470 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8201 (mp0) REVERT: H 484 MET cc_start: 0.8233 (mpp) cc_final: 0.7643 (mpp) REVERT: H 485 ILE cc_start: 0.9474 (mm) cc_final: 0.9210 (tp) REVERT: H 488 ILE cc_start: 0.8625 (tt) cc_final: 0.8305 (tt) REVERT: H 499 LEU cc_start: 0.8844 (mp) cc_final: 0.8440 (mp) REVERT: H 521 LEU cc_start: 0.9518 (mm) cc_final: 0.9102 (mm) REVERT: H 529 ILE cc_start: 0.8700 (mp) cc_final: 0.8121 (tp) REVERT: H 568 GLN cc_start: 0.8573 (pp30) cc_final: 0.6348 (pp30) REVERT: H 583 ILE cc_start: 0.9002 (mp) cc_final: 0.8794 (pt) REVERT: H 584 THR cc_start: 0.8106 (p) cc_final: 0.7822 (p) REVERT: H 605 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8835 (pt0) REVERT: H 611 GLN cc_start: 0.8429 (tp40) cc_final: 0.8098 (tp40) REVERT: H 622 LEU cc_start: 0.9421 (mm) cc_final: 0.9178 (mm) REVERT: H 736 PHE cc_start: 0.8937 (t80) cc_final: 0.8526 (t80) REVERT: H 737 PHE cc_start: 0.9146 (m-80) cc_final: 0.8552 (m-80) REVERT: H 744 MET cc_start: 0.9117 (ptt) cc_final: 0.8905 (ptt) REVERT: H 745 HIS cc_start: 0.8796 (m-70) cc_final: 0.8503 (m90) REVERT: I 149 TYR cc_start: 0.9252 (t80) cc_final: 0.8942 (t80) REVERT: I 154 ILE cc_start: 0.9334 (mm) cc_final: 0.9026 (mm) REVERT: I 157 ARG cc_start: 0.8509 (ttp80) cc_final: 0.7868 (ttp80) REVERT: I 158 ASP cc_start: 0.8874 (m-30) cc_final: 0.8484 (m-30) REVERT: I 205 PHE cc_start: 0.8402 (m-80) cc_final: 0.8016 (m-80) REVERT: I 230 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.7512 (tpp80) REVERT: I 244 MET cc_start: 0.9548 (tpt) cc_final: 0.9135 (tpt) REVERT: I 259 LEU cc_start: 0.9288 (pp) cc_final: 0.9040 (mt) REVERT: I 264 MET cc_start: 0.8329 (pmm) cc_final: 0.7600 (pmm) REVERT: I 268 TYR cc_start: 0.8934 (m-10) cc_final: 0.8694 (m-80) REVERT: I 440 ASN cc_start: 0.7446 (m-40) cc_final: 0.7080 (m-40) REVERT: J 157 ARG cc_start: 0.8920 (ptt-90) cc_final: 0.8494 (ptt-90) REVERT: J 174 LEU cc_start: 0.8849 (mm) cc_final: 0.8640 (pp) REVERT: J 201 PHE cc_start: 0.8845 (m-80) cc_final: 0.8451 (m-10) REVERT: J 205 PHE cc_start: 0.8941 (m-80) cc_final: 0.8465 (m-10) REVERT: J 217 PHE cc_start: 0.9067 (t80) cc_final: 0.8351 (t80) REVERT: J 221 PHE cc_start: 0.8751 (t80) cc_final: 0.8168 (t80) REVERT: J 247 PHE cc_start: 0.9092 (m-80) cc_final: 0.8693 (m-10) REVERT: J 277 HIS cc_start: 0.9057 (t-90) cc_final: 0.8809 (t-90) REVERT: J 411 GLN cc_start: 0.8776 (tp-100) cc_final: 0.8439 (pt0) REVERT: J 436 TYR cc_start: 0.6673 (m-10) cc_final: 0.6363 (m-80) outliers start: 0 outliers final: 0 residues processed: 969 average time/residue: 0.5483 time to fit residues: 868.8435 Evaluate side-chains 820 residues out of total 5211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 820 time to evaluate : 5.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 359 optimal weight: 1.9990 chunk 481 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 416 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 452 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 465 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 HIS ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN C 485 GLN D 263 HIS ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN E 553 ASN F 299 HIS F 328 ASN F 499 ASN G 211 HIS ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 563 GLN H 594 ASN H 638 ASN H 732 ASN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 HIS ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.159178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.105877 restraints weight = 98036.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.108774 restraints weight = 55494.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.111422 restraints weight = 32256.505| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 42867 Z= 0.188 Angle : 0.611 10.303 58454 Z= 0.317 Chirality : 0.045 0.235 6899 Planarity : 0.004 0.069 7709 Dihedral : 4.639 22.926 6111 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.02 % Allowed : 0.37 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.55 (0.11), residues: 5708 helix: 0.36 (0.13), residues: 1599 sheet: -0.32 (0.16), residues: 1060 loop : -0.71 (0.11), residues: 3049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 346 HIS 0.005 0.001 HIS E 336 PHE 0.028 0.001 PHE I 471 TYR 0.061 0.002 TYR I 167 ARG 0.013 0.001 ARG C 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12879.64 seconds wall clock time: 231 minutes 59.76 seconds (13919.76 seconds total)