Starting phenix.real_space_refine on Mon Mar 25 06:52:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9h_20700/03_2024/6u9h_20700_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9h_20700/03_2024/6u9h_20700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9h_20700/03_2024/6u9h_20700.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9h_20700/03_2024/6u9h_20700.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9h_20700/03_2024/6u9h_20700_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9h_20700/03_2024/6u9h_20700_neut_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 8 5.21 5 S 236 5.16 5 C 29260 2.51 5 N 8068 2.21 5 O 8752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 213": "OE1" <-> "OE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 375": "OD1" <-> "OD2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 536": "OD1" <-> "OD2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 638": "OD1" <-> "OD2" Residue "A ASP 659": "OD1" <-> "OD2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B ASP 375": "OD1" <-> "OD2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ASP 397": "OD1" <-> "OD2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B ASP 595": "OD1" <-> "OD2" Residue "B PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 638": "OD1" <-> "OD2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F GLU 161": "OE1" <-> "OE2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "F ARG 218": "NH1" <-> "NH2" Residue "F ARG 226": "NH1" <-> "NH2" Residue "F ARG 237": "NH1" <-> "NH2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "G ASP 313": "OD1" <-> "OD2" Residue "G ARG 343": "NH1" <-> "NH2" Residue "G GLU 356": "OE1" <-> "OE2" Residue "G GLU 402": "OE1" <-> "OE2" Residue "G ARG 415": "NH1" <-> "NH2" Residue "G ARG 416": "NH1" <-> "NH2" Residue "G ASP 417": "OD1" <-> "OD2" Residue "G ARG 453": "NH1" <-> "NH2" Residue "G ARG 473": "NH1" <-> "NH2" Residue "H ASP 181": "OD1" <-> "OD2" Residue "H PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 253": "OD1" <-> "OD2" Residue "H ARG 279": "NH1" <-> "NH2" Residue "H ASP 315": "OD1" <-> "OD2" Residue "H ASP 342": "OD1" <-> "OD2" Residue "H TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 375": "OD1" <-> "OD2" Residue "H ASP 376": "OD1" <-> "OD2" Residue "H ARG 377": "NH1" <-> "NH2" Residue "H ARG 388": "NH1" <-> "NH2" Residue "H ASP 397": "OD1" <-> "OD2" Residue "H ARG 429": "NH1" <-> "NH2" Residue "H PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 536": "OD1" <-> "OD2" Residue "H GLU 575": "OE1" <-> "OE2" Residue "H PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 90": "NH1" <-> "NH2" Residue "I ASP 181": "OD1" <-> "OD2" Residue "I GLU 208": "OE1" <-> "OE2" Residue "I ARG 216": "NH1" <-> "NH2" Residue "I PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 253": "OD1" <-> "OD2" Residue "I GLU 343": "OE1" <-> "OE2" Residue "I ARG 388": "NH1" <-> "NH2" Residue "I ASP 397": "OD1" <-> "OD2" Residue "I ARG 429": "NH1" <-> "NH2" Residue "I TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 547": "OE1" <-> "OE2" Residue "I PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 594": "OE1" <-> "OE2" Residue "I ASP 595": "OD1" <-> "OD2" Residue "I PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 620": "OD1" <-> "OD2" Residue "I GLU 663": "OE1" <-> "OE2" Residue "J ARG 110": "NH1" <-> "NH2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "J GLU 165": "OE1" <-> "OE2" Residue "J ARG 218": "NH1" <-> "NH2" Residue "J ARG 226": "NH1" <-> "NH2" Residue "J ARG 237": "NH1" <-> "NH2" Residue "J ARG 238": "NH1" <-> "NH2" Residue "K ASP 313": "OD1" <-> "OD2" Residue "K ARG 343": "NH1" <-> "NH2" Residue "K GLU 356": "OE1" <-> "OE2" Residue "K GLU 402": "OE1" <-> "OE2" Residue "K ARG 415": "NH1" <-> "NH2" Residue "K ARG 416": "NH1" <-> "NH2" Residue "K ASP 417": "OD1" <-> "OD2" Residue "K ARG 453": "NH1" <-> "NH2" Residue "K ARG 473": "NH1" <-> "NH2" Residue "L GLU 152": "OE1" <-> "OE2" Residue "L ASP 181": "OD1" <-> "OD2" Residue "L GLU 213": "OE1" <-> "OE2" Residue "L GLU 229": "OE1" <-> "OE2" Residue "L PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 253": "OD1" <-> "OD2" Residue "L ASP 257": "OD1" <-> "OD2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "L ARG 279": "NH1" <-> "NH2" Residue "L GLU 298": "OE1" <-> "OE2" Residue "L ASP 315": "OD1" <-> "OD2" Residue "L ASP 342": "OD1" <-> "OD2" Residue "L TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 375": "OD1" <-> "OD2" Residue "L ARG 377": "NH1" <-> "NH2" Residue "L ARG 388": "NH1" <-> "NH2" Residue "L ASP 397": "OD1" <-> "OD2" Residue "L ARG 429": "NH1" <-> "NH2" Residue "L PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 536": "OD1" <-> "OD2" Residue "L GLU 575": "OE1" <-> "OE2" Residue "L PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 638": "OD1" <-> "OD2" Residue "M ARG 90": "NH1" <-> "NH2" Residue "M GLU 152": "OE1" <-> "OE2" Residue "M ASP 181": "OD1" <-> "OD2" Residue "M GLU 208": "OE1" <-> "OE2" Residue "M ARG 216": "NH1" <-> "NH2" Residue "M GLU 343": "OE1" <-> "OE2" Residue "M ASP 375": "OD1" <-> "OD2" Residue "M ARG 388": "NH1" <-> "NH2" Residue "M ARG 429": "NH1" <-> "NH2" Residue "M TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 547": "OE1" <-> "OE2" Residue "M GLU 594": "OE1" <-> "OE2" Residue "M ASP 595": "OD1" <-> "OD2" Residue "M PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 659": "OD1" <-> "OD2" Residue "M GLU 663": "OE1" <-> "OE2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "N GLU 161": "OE1" <-> "OE2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "N ARG 218": "NH1" <-> "NH2" Residue "N ARG 226": "NH1" <-> "NH2" Residue "N ARG 237": "NH1" <-> "NH2" Residue "N ARG 238": "NH1" <-> "NH2" Residue "O ASP 313": "OD1" <-> "OD2" Residue "O ARG 343": "NH1" <-> "NH2" Residue "O GLU 356": "OE1" <-> "OE2" Residue "O GLU 402": "OE1" <-> "OE2" Residue "O ARG 415": "NH1" <-> "NH2" Residue "O ARG 416": "NH1" <-> "NH2" Residue "O ASP 417": "OD1" <-> "OD2" Residue "O ARG 453": "NH1" <-> "NH2" Residue "O ARG 473": "NH1" <-> "NH2" Residue "P GLU 229": "OE1" <-> "OE2" Residue "P PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 253": "OD1" <-> "OD2" Residue "P GLU 268": "OE1" <-> "OE2" Residue "P ARG 279": "NH1" <-> "NH2" Residue "P GLU 298": "OE1" <-> "OE2" Residue "P ASP 315": "OD1" <-> "OD2" Residue "P ASP 342": "OD1" <-> "OD2" Residue "P TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 375": "OD1" <-> "OD2" Residue "P ASP 376": "OD1" <-> "OD2" Residue "P ARG 377": "NH1" <-> "NH2" Residue "P ARG 388": "NH1" <-> "NH2" Residue "P ARG 429": "NH1" <-> "NH2" Residue "P PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 536": "OD1" <-> "OD2" Residue "P GLU 575": "OE1" <-> "OE2" Residue "P PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 90": "NH1" <-> "NH2" Residue "Q GLU 152": "OE1" <-> "OE2" Residue "Q ASP 181": "OD1" <-> "OD2" Residue "Q GLU 208": "OE1" <-> "OE2" Residue "Q ARG 216": "NH1" <-> "NH2" Residue "Q ASP 253": "OD1" <-> "OD2" Residue "Q GLU 343": "OE1" <-> "OE2" Residue "Q ARG 388": "NH1" <-> "NH2" Residue "Q ASP 397": "OD1" <-> "OD2" Residue "Q ARG 429": "NH1" <-> "NH2" Residue "Q TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 547": "OE1" <-> "OE2" Residue "Q PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 594": "OE1" <-> "OE2" Residue "Q ASP 595": "OD1" <-> "OD2" Residue "Q PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 638": "OD1" <-> "OD2" Residue "Q GLU 663": "OE1" <-> "OE2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "R GLU 161": "OE1" <-> "OE2" Residue "R GLU 165": "OE1" <-> "OE2" Residue "R ARG 218": "NH1" <-> "NH2" Residue "R ARG 226": "NH1" <-> "NH2" Residue "R ARG 237": "NH1" <-> "NH2" Residue "R ARG 238": "NH1" <-> "NH2" Residue "S ASP 313": "OD1" <-> "OD2" Residue "S ARG 343": "NH1" <-> "NH2" Residue "S GLU 356": "OE1" <-> "OE2" Residue "S GLU 402": "OE1" <-> "OE2" Residue "S ARG 415": "NH1" <-> "NH2" Residue "S ARG 416": "NH1" <-> "NH2" Residue "S ASP 417": "OD1" <-> "OD2" Residue "S ARG 453": "NH1" <-> "NH2" Residue "S ARG 473": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46356 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4451 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4528 Chain: "B" Number of atoms: 4451 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4528 Chain: "F" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 3, 'TRANS': 151} Chain: "G" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1297 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "H" Number of atoms: 4451 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4528 Chain: "I" Number of atoms: 4451 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4528 Chain: "J" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 3, 'TRANS': 151} Chain: "K" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1297 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "L" Number of atoms: 4451 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4528 Chain: "M" Number of atoms: 4451 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4528 Chain: "N" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 3, 'TRANS': 151} Chain: "O" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1297 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "P" Number of atoms: 4451 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4528 Chain: "Q" Number of atoms: 4451 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 582, 4442 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 544} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4528 Chain: "R" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 3, 'TRANS': 151} Chain: "S" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1297 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AGLU A 208 " occ=0.35 ... (16 atoms not shown) pdb=" OE2BGLU A 208 " occ=0.65 residue: pdb=" N AGLU B 208 " occ=0.35 ... (16 atoms not shown) pdb=" OE2BGLU B 208 " occ=0.65 residue: pdb=" N AGLU H 208 " occ=0.35 ... (16 atoms not shown) pdb=" OE2BGLU H 208 " occ=0.65 residue: pdb=" N AGLU I 208 " occ=0.35 ... (16 atoms not shown) pdb=" OE2BGLU I 208 " occ=0.65 residue: pdb=" N AGLU L 208 " occ=0.35 ... (16 atoms not shown) pdb=" OE2BGLU L 208 " occ=0.65 residue: pdb=" N AGLU M 208 " occ=0.35 ... (16 atoms not shown) pdb=" OE2BGLU M 208 " occ=0.65 residue: pdb=" N AGLU P 208 " occ=0.35 ... (16 atoms not shown) pdb=" OE2BGLU P 208 " occ=0.65 residue: pdb=" N AGLU Q 208 " occ=0.35 ... (16 atoms not shown) pdb=" OE2BGLU Q 208 " occ=0.65 Time building chain proxies: 38.68, per 1000 atoms: 0.83 Number of scatterers: 46356 At special positions: 0 Unit cell: (215, 215, 93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 236 16.00 P 32 15.00 Mg 8 11.99 O 8752 8.00 N 8068 7.00 C 29260 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: 19.63 Conformation dependent library (CDL) restraints added in 15.6 seconds 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 233 helices and 48 sheets defined 33.8% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.31 Creating SS restraints... Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 124 through 131 Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 176 through 184 removed outlier: 3.550A pdb=" N LEU A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 217 removed outlier: 3.898A pdb=" N ARG A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N SER A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 256 through 259 No H-bonds generated for 'chain 'A' and resid 256 through 259' Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 290 through 296 removed outlier: 4.161A pdb=" N LEU A 295 " --> pdb=" O GLN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 removed outlier: 3.541A pdb=" N LEU A 311 " --> pdb=" O GLY A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 376 through 379 No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 438 through 450 removed outlier: 3.882A pdb=" N GLU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 450 " --> pdb=" O VAL A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 474 removed outlier: 3.796A pdb=" N LYS A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 493 removed outlier: 3.565A pdb=" N ALA A 492 " --> pdb=" O HIS A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.543A pdb=" N GLY A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 554 removed outlier: 3.657A pdb=" N ASN A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLN A 546 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU A 547 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ALA A 549 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR A 550 " --> pdb=" O GLN A 546 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 576 removed outlier: 4.266A pdb=" N GLN A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 605 Processing helix chain 'A' and resid 618 through 628 removed outlier: 3.863A pdb=" N ARG A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.648A pdb=" N VAL B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 removed outlier: 3.631A pdb=" N LEU B 130 " --> pdb=" O HIS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 172 through 184 removed outlier: 4.045A pdb=" N VAL B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY B 178 " --> pdb=" O ASN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 214 No H-bonds generated for 'chain 'B' and resid 211 through 214' Processing helix chain 'B' and resid 228 through 243 Proline residue: B 232 - end of helix Processing helix chain 'B' and resid 256 through 260 Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.946A pdb=" N ARG B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 297 removed outlier: 3.734A pdb=" N GLN B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 292 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 297 " --> pdb=" O VAL B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.610A pdb=" N ASN B 312 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 323 removed outlier: 3.762A pdb=" N PHE B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 removed outlier: 4.425A pdb=" N ALA B 360 " --> pdb=" O TYR B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 379 No H-bonds generated for 'chain 'B' and resid 376 through 379' Processing helix chain 'B' and resid 415 through 428 removed outlier: 3.961A pdb=" N GLN B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 426 " --> pdb=" O MET B 422 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN B 428 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.732A pdb=" N LEU B 444 " --> pdb=" O TRP B 440 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 473 removed outlier: 3.908A pdb=" N ILE B 468 " --> pdb=" O PRO B 464 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 493 removed outlier: 3.969A pdb=" N ALA B 492 " --> pdb=" O HIS B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 526 removed outlier: 3.618A pdb=" N ILE B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 525 " --> pdb=" O ILE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 544 removed outlier: 4.443A pdb=" N ILE B 542 " --> pdb=" O ASP B 538 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASN B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 552 removed outlier: 3.806A pdb=" N ARG B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 578 removed outlier: 3.751A pdb=" N ARG B 577 " --> pdb=" O GLN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 608 Processing helix chain 'B' and resid 618 through 620 No H-bonds generated for 'chain 'B' and resid 618 through 620' Processing helix chain 'B' and resid 623 through 630 removed outlier: 3.573A pdb=" N LEU B 629 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 659 No H-bonds generated for 'chain 'B' and resid 657 through 659' Processing helix chain 'F' and resid 99 through 108 removed outlier: 3.608A pdb=" N ALA F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 145 removed outlier: 3.707A pdb=" N GLU F 144 " --> pdb=" O GLN F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 188 removed outlier: 3.863A pdb=" N ALA F 181 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU F 182 " --> pdb=" O GLU F 178 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TRP F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 222 removed outlier: 4.219A pdb=" N LYS F 221 " --> pdb=" O GLU F 217 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 342 removed outlier: 3.651A pdb=" N VAL G 339 " --> pdb=" O ILE G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 371 through 383 removed outlier: 4.020A pdb=" N GLN G 379 " --> pdb=" O SER G 375 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLN G 380 " --> pdb=" O LYS G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 395 No H-bonds generated for 'chain 'G' and resid 393 through 395' Processing helix chain 'G' and resid 412 through 424 removed outlier: 3.543A pdb=" N ARG G 416 " --> pdb=" O ALA G 412 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP G 417 " --> pdb=" O ALA G 413 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP G 420 " --> pdb=" O ARG G 416 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ILE G 421 " --> pdb=" O ASP G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 455 Processing helix chain 'H' and resid 99 through 110 Processing helix chain 'H' and resid 124 through 131 Processing helix chain 'H' and resid 144 through 155 Processing helix chain 'H' and resid 170 through 184 removed outlier: 3.740A pdb=" N VAL H 176 " --> pdb=" O ALA H 172 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER H 177 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY H 178 " --> pdb=" O ASN H 174 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 216 removed outlier: 3.959A pdb=" N ARG H 216 " --> pdb=" O VAL H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 243 Processing helix chain 'H' and resid 256 through 259 No H-bonds generated for 'chain 'H' and resid 256 through 259' Processing helix chain 'H' and resid 276 through 278 No H-bonds generated for 'chain 'H' and resid 276 through 278' Processing helix chain 'H' and resid 290 through 296 removed outlier: 4.210A pdb=" N LEU H 295 " --> pdb=" O GLN H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 311 removed outlier: 3.557A pdb=" N LEU H 311 " --> pdb=" O GLY H 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 308 through 311' Processing helix chain 'H' and resid 316 through 324 Processing helix chain 'H' and resid 355 through 361 Processing helix chain 'H' and resid 376 through 379 No H-bonds generated for 'chain 'H' and resid 376 through 379' Processing helix chain 'H' and resid 415 through 420 Processing helix chain 'H' and resid 426 through 428 No H-bonds generated for 'chain 'H' and resid 426 through 428' Processing helix chain 'H' and resid 438 through 450 removed outlier: 3.940A pdb=" N GLU H 443 " --> pdb=" O VAL H 439 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU H 444 " --> pdb=" O TRP H 440 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLN H 449 " --> pdb=" O ASN H 445 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS H 450 " --> pdb=" O VAL H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 464 through 474 removed outlier: 3.786A pdb=" N LYS H 469 " --> pdb=" O GLN H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 493 removed outlier: 3.547A pdb=" N TRP H 491 " --> pdb=" O GLN H 487 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA H 492 " --> pdb=" O HIS H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 516 through 526 removed outlier: 3.514A pdb=" N VAL H 525 " --> pdb=" O ILE H 521 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 554 removed outlier: 3.702A pdb=" N ASN H 544 " --> pdb=" O SER H 540 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLN H 546 " --> pdb=" O ILE H 542 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLU H 547 " --> pdb=" O MET H 543 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU H 548 " --> pdb=" O ASN H 544 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA H 549 " --> pdb=" O VAL H 545 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR H 550 " --> pdb=" O GLN H 546 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE H 551 " --> pdb=" O GLU H 547 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG H 552 " --> pdb=" O LEU H 548 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL H 553 " --> pdb=" O ALA H 549 " (cutoff:3.500A) Processing helix chain 'H' and resid 569 through 576 removed outlier: 4.236A pdb=" N GLN H 573 " --> pdb=" O GLY H 569 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP H 576 " --> pdb=" O MET H 572 " (cutoff:3.500A) Processing helix chain 'H' and resid 602 through 605 No H-bonds generated for 'chain 'H' and resid 602 through 605' Processing helix chain 'H' and resid 618 through 628 removed outlier: 3.868A pdb=" N ARG H 622 " --> pdb=" O LYS H 618 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU H 623 " --> pdb=" O ALA H 619 " (cutoff:3.500A) Processing helix chain 'H' and resid 657 through 659 No H-bonds generated for 'chain 'H' and resid 657 through 659' Processing helix chain 'I' and resid 99 through 110 removed outlier: 3.660A pdb=" N VAL I 104 " --> pdb=" O ALA I 100 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU I 105 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 130 removed outlier: 3.516A pdb=" N LEU I 130 " --> pdb=" O HIS I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 156 removed outlier: 3.857A pdb=" N ALA I 155 " --> pdb=" O ALA I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 184 removed outlier: 3.916A pdb=" N VAL I 176 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N SER I 177 " --> pdb=" O THR I 173 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY I 178 " --> pdb=" O ASN I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 214 No H-bonds generated for 'chain 'I' and resid 211 through 214' Processing helix chain 'I' and resid 228 through 243 Proline residue: I 232 - end of helix Processing helix chain 'I' and resid 256 through 260 Processing helix chain 'I' and resid 274 through 279 removed outlier: 3.882A pdb=" N ARG I 279 " --> pdb=" O GLY I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 297 removed outlier: 3.824A pdb=" N GLN I 291 " --> pdb=" O SER I 287 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE I 292 " --> pdb=" O HIS I 288 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER I 297 " --> pdb=" O VAL I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 312 removed outlier: 3.665A pdb=" N ASN I 312 " --> pdb=" O GLY I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 316 through 323 removed outlier: 3.768A pdb=" N PHE I 320 " --> pdb=" O GLU I 316 " (cutoff:3.500A) Processing helix chain 'I' and resid 355 through 362 removed outlier: 4.449A pdb=" N ALA I 360 " --> pdb=" O TYR I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 376 through 379 No H-bonds generated for 'chain 'I' and resid 376 through 379' Processing helix chain 'I' and resid 415 through 428 removed outlier: 3.980A pdb=" N GLN I 420 " --> pdb=" O LYS I 416 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS I 424 " --> pdb=" O GLN I 420 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU I 426 " --> pdb=" O MET I 422 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN I 428 " --> pdb=" O LYS I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 448 removed outlier: 3.711A pdb=" N LEU I 444 " --> pdb=" O TRP I 440 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN I 447 " --> pdb=" O GLU I 443 " (cutoff:3.500A) Processing helix chain 'I' and resid 464 through 473 removed outlier: 3.947A pdb=" N ILE I 468 " --> pdb=" O PRO I 464 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU I 473 " --> pdb=" O LYS I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 487 through 493 removed outlier: 4.071A pdb=" N ALA I 492 " --> pdb=" O HIS I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 515 through 526 removed outlier: 3.678A pdb=" N ILE I 521 " --> pdb=" O LEU I 517 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL I 525 " --> pdb=" O ILE I 521 " (cutoff:3.500A) Processing helix chain 'I' and resid 538 through 544 removed outlier: 4.451A pdb=" N ILE I 542 " --> pdb=" O ASP I 538 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN I 544 " --> pdb=" O SER I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 547 through 552 removed outlier: 3.915A pdb=" N ARG I 552 " --> pdb=" O LEU I 548 " (cutoff:3.500A) Processing helix chain 'I' and resid 569 through 578 removed outlier: 3.781A pdb=" N ARG I 577 " --> pdb=" O GLN I 573 " (cutoff:3.500A) Processing helix chain 'I' and resid 602 through 608 Processing helix chain 'I' and resid 618 through 620 No H-bonds generated for 'chain 'I' and resid 618 through 620' Processing helix chain 'I' and resid 623 through 630 removed outlier: 3.516A pdb=" N LEU I 629 " --> pdb=" O ILE I 625 " (cutoff:3.500A) Processing helix chain 'I' and resid 657 through 659 No H-bonds generated for 'chain 'I' and resid 657 through 659' Processing helix chain 'J' and resid 99 through 108 removed outlier: 3.608A pdb=" N ALA J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 145 removed outlier: 3.706A pdb=" N GLU J 144 " --> pdb=" O GLN J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 188 removed outlier: 3.862A pdb=" N ALA J 181 " --> pdb=" O PRO J 177 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU J 182 " --> pdb=" O GLU J 178 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE J 183 " --> pdb=" O SER J 179 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TRP J 185 " --> pdb=" O ALA J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 222 removed outlier: 4.218A pdb=" N LYS J 221 " --> pdb=" O GLU J 217 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS J 222 " --> pdb=" O ARG J 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 342 removed outlier: 3.652A pdb=" N VAL K 339 " --> pdb=" O ILE K 335 " (cutoff:3.500A) Processing helix chain 'K' and resid 371 through 383 removed outlier: 4.020A pdb=" N GLN K 379 " --> pdb=" O SER K 375 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLN K 380 " --> pdb=" O LYS K 376 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 395 No H-bonds generated for 'chain 'K' and resid 393 through 395' Processing helix chain 'K' and resid 412 through 424 removed outlier: 3.543A pdb=" N ARG K 416 " --> pdb=" O ALA K 412 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP K 417 " --> pdb=" O ALA K 413 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP K 420 " --> pdb=" O ARG K 416 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ILE K 421 " --> pdb=" O ASP K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 445 through 455 Processing helix chain 'L' and resid 99 through 110 Processing helix chain 'L' and resid 124 through 131 Processing helix chain 'L' and resid 144 through 155 Processing helix chain 'L' and resid 170 through 184 removed outlier: 3.816A pdb=" N VAL L 176 " --> pdb=" O ALA L 172 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER L 177 " --> pdb=" O THR L 173 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLY L 178 " --> pdb=" O ASN L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 216 removed outlier: 3.920A pdb=" N ARG L 216 " --> pdb=" O VAL L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 231 through 243 Processing helix chain 'L' and resid 256 through 259 No H-bonds generated for 'chain 'L' and resid 256 through 259' Processing helix chain 'L' and resid 276 through 278 No H-bonds generated for 'chain 'L' and resid 276 through 278' Processing helix chain 'L' and resid 290 through 296 removed outlier: 4.182A pdb=" N LEU L 295 " --> pdb=" O GLN L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 311 removed outlier: 3.557A pdb=" N LEU L 311 " --> pdb=" O GLY L 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 308 through 311' Processing helix chain 'L' and resid 316 through 324 Processing helix chain 'L' and resid 355 through 361 Processing helix chain 'L' and resid 376 through 379 No H-bonds generated for 'chain 'L' and resid 376 through 379' Processing helix chain 'L' and resid 415 through 420 Processing helix chain 'L' and resid 426 through 428 No H-bonds generated for 'chain 'L' and resid 426 through 428' Processing helix chain 'L' and resid 438 through 450 removed outlier: 3.939A pdb=" N GLU L 443 " --> pdb=" O VAL L 439 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU L 444 " --> pdb=" O TRP L 440 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN L 449 " --> pdb=" O ASN L 445 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS L 450 " --> pdb=" O VAL L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 464 through 474 removed outlier: 3.773A pdb=" N LYS L 469 " --> pdb=" O GLN L 465 " (cutoff:3.500A) Processing helix chain 'L' and resid 487 through 493 removed outlier: 3.804A pdb=" N ALA L 492 " --> pdb=" O HIS L 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 516 through 526 Processing helix chain 'L' and resid 540 through 554 removed outlier: 3.674A pdb=" N ASN L 544 " --> pdb=" O SER L 540 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLN L 546 " --> pdb=" O ILE L 542 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLU L 547 " --> pdb=" O MET L 543 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LEU L 548 " --> pdb=" O ASN L 544 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA L 549 " --> pdb=" O VAL L 545 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR L 550 " --> pdb=" O GLN L 546 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE L 551 " --> pdb=" O GLU L 547 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG L 552 " --> pdb=" O LEU L 548 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL L 553 " --> pdb=" O ALA L 549 " (cutoff:3.500A) Processing helix chain 'L' and resid 569 through 576 removed outlier: 4.237A pdb=" N GLN L 573 " --> pdb=" O GLY L 569 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP L 576 " --> pdb=" O MET L 572 " (cutoff:3.500A) Processing helix chain 'L' and resid 602 through 605 No H-bonds generated for 'chain 'L' and resid 602 through 605' Processing helix chain 'L' and resid 618 through 628 removed outlier: 3.850A pdb=" N ARG L 622 " --> pdb=" O LYS L 618 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU L 623 " --> pdb=" O ALA L 619 " (cutoff:3.500A) Processing helix chain 'L' and resid 657 through 659 No H-bonds generated for 'chain 'L' and resid 657 through 659' Processing helix chain 'M' and resid 99 through 110 removed outlier: 3.708A pdb=" N VAL M 104 " --> pdb=" O ALA M 100 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU M 105 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 130 removed outlier: 3.596A pdb=" N LEU M 130 " --> pdb=" O HIS M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 156 removed outlier: 3.693A pdb=" N GLU M 152 " --> pdb=" O VAL M 148 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA M 155 " --> pdb=" O ALA M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 184 removed outlier: 3.888A pdb=" N VAL M 176 " --> pdb=" O ALA M 172 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N SER M 177 " --> pdb=" O THR M 173 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY M 178 " --> pdb=" O ASN M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 214 No H-bonds generated for 'chain 'M' and resid 211 through 214' Processing helix chain 'M' and resid 228 through 243 Proline residue: M 232 - end of helix Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 274 through 279 removed outlier: 3.909A pdb=" N ARG M 279 " --> pdb=" O GLY M 275 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 297 removed outlier: 3.798A pdb=" N GLN M 291 " --> pdb=" O SER M 287 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE M 292 " --> pdb=" O HIS M 288 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER M 297 " --> pdb=" O VAL M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 312 removed outlier: 3.645A pdb=" N ASN M 312 " --> pdb=" O GLY M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 316 through 323 removed outlier: 3.767A pdb=" N PHE M 320 " --> pdb=" O GLU M 316 " (cutoff:3.500A) Processing helix chain 'M' and resid 355 through 362 removed outlier: 4.448A pdb=" N ALA M 360 " --> pdb=" O TYR M 356 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL M 361 " --> pdb=" O ALA M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 376 through 379 No H-bonds generated for 'chain 'M' and resid 376 through 379' Processing helix chain 'M' and resid 415 through 428 removed outlier: 3.953A pdb=" N GLN M 420 " --> pdb=" O LYS M 416 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS M 424 " --> pdb=" O GLN M 420 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU M 426 " --> pdb=" O MET M 422 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN M 428 " --> pdb=" O LYS M 424 " (cutoff:3.500A) Processing helix chain 'M' and resid 438 through 448 removed outlier: 3.695A pdb=" N LEU M 444 " --> pdb=" O TRP M 440 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN M 447 " --> pdb=" O GLU M 443 " (cutoff:3.500A) Processing helix chain 'M' and resid 464 through 473 removed outlier: 3.954A pdb=" N ILE M 468 " --> pdb=" O PRO M 464 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU M 473 " --> pdb=" O LYS M 469 " (cutoff:3.500A) Processing helix chain 'M' and resid 487 through 493 removed outlier: 3.987A pdb=" N ALA M 492 " --> pdb=" O HIS M 488 " (cutoff:3.500A) Processing helix chain 'M' and resid 516 through 526 removed outlier: 3.690A pdb=" N ILE M 521 " --> pdb=" O LEU M 517 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL M 525 " --> pdb=" O ILE M 521 " (cutoff:3.500A) Processing helix chain 'M' and resid 538 through 544 removed outlier: 4.429A pdb=" N ILE M 542 " --> pdb=" O ASP M 538 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN M 544 " --> pdb=" O SER M 540 " (cutoff:3.500A) Processing helix chain 'M' and resid 547 through 552 removed outlier: 3.763A pdb=" N ARG M 552 " --> pdb=" O LEU M 548 " (cutoff:3.500A) Processing helix chain 'M' and resid 569 through 578 removed outlier: 3.868A pdb=" N ARG M 577 " --> pdb=" O GLN M 573 " (cutoff:3.500A) Processing helix chain 'M' and resid 602 through 608 Processing helix chain 'M' and resid 618 through 620 No H-bonds generated for 'chain 'M' and resid 618 through 620' Processing helix chain 'M' and resid 623 through 630 removed outlier: 3.632A pdb=" N LEU M 629 " --> pdb=" O ILE M 625 " (cutoff:3.500A) Processing helix chain 'M' and resid 657 through 659 No H-bonds generated for 'chain 'M' and resid 657 through 659' Processing helix chain 'N' and resid 99 through 108 removed outlier: 3.609A pdb=" N ALA N 108 " --> pdb=" O ALA N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 145 removed outlier: 3.707A pdb=" N GLU N 144 " --> pdb=" O GLN N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 188 removed outlier: 3.863A pdb=" N ALA N 181 " --> pdb=" O PRO N 177 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU N 182 " --> pdb=" O GLU N 178 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE N 183 " --> pdb=" O SER N 179 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TRP N 185 " --> pdb=" O ALA N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 222 removed outlier: 4.218A pdb=" N LYS N 221 " --> pdb=" O GLU N 217 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS N 222 " --> pdb=" O ARG N 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 332 through 342 removed outlier: 3.652A pdb=" N VAL O 339 " --> pdb=" O ILE O 335 " (cutoff:3.500A) Processing helix chain 'O' and resid 371 through 383 removed outlier: 4.019A pdb=" N GLN O 379 " --> pdb=" O SER O 375 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLN O 380 " --> pdb=" O LYS O 376 " (cutoff:3.500A) Processing helix chain 'O' and resid 393 through 395 No H-bonds generated for 'chain 'O' and resid 393 through 395' Processing helix chain 'O' and resid 412 through 424 removed outlier: 3.544A pdb=" N ARG O 416 " --> pdb=" O ALA O 412 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP O 417 " --> pdb=" O ALA O 413 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP O 420 " --> pdb=" O ARG O 416 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE O 421 " --> pdb=" O ASP O 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 445 through 455 Processing helix chain 'P' and resid 99 through 110 Processing helix chain 'P' and resid 124 through 131 Processing helix chain 'P' and resid 144 through 155 Processing helix chain 'P' and resid 170 through 184 removed outlier: 3.804A pdb=" N VAL P 176 " --> pdb=" O ALA P 172 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER P 177 " --> pdb=" O THR P 173 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLY P 178 " --> pdb=" O ASN P 174 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU P 184 " --> pdb=" O ALA P 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 217 removed outlier: 3.955A pdb=" N ARG P 216 " --> pdb=" O VAL P 212 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER P 217 " --> pdb=" O GLU P 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 231 through 243 Processing helix chain 'P' and resid 256 through 259 No H-bonds generated for 'chain 'P' and resid 256 through 259' Processing helix chain 'P' and resid 276 through 278 No H-bonds generated for 'chain 'P' and resid 276 through 278' Processing helix chain 'P' and resid 290 through 296 removed outlier: 4.155A pdb=" N LEU P 295 " --> pdb=" O GLN P 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 308 through 311 removed outlier: 3.528A pdb=" N LEU P 311 " --> pdb=" O GLY P 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 308 through 311' Processing helix chain 'P' and resid 316 through 324 Processing helix chain 'P' and resid 355 through 361 Processing helix chain 'P' and resid 376 through 379 No H-bonds generated for 'chain 'P' and resid 376 through 379' Processing helix chain 'P' and resid 415 through 420 Processing helix chain 'P' and resid 426 through 428 No H-bonds generated for 'chain 'P' and resid 426 through 428' Processing helix chain 'P' and resid 438 through 450 removed outlier: 3.836A pdb=" N GLU P 443 " --> pdb=" O VAL P 439 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU P 444 " --> pdb=" O TRP P 440 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN P 449 " --> pdb=" O ASN P 445 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS P 450 " --> pdb=" O VAL P 446 " (cutoff:3.500A) Processing helix chain 'P' and resid 464 through 474 removed outlier: 3.793A pdb=" N LYS P 469 " --> pdb=" O GLN P 465 " (cutoff:3.500A) Processing helix chain 'P' and resid 487 through 493 removed outlier: 3.596A pdb=" N ALA P 492 " --> pdb=" O HIS P 488 " (cutoff:3.500A) Processing helix chain 'P' and resid 516 through 526 removed outlier: 3.505A pdb=" N ILE P 521 " --> pdb=" O LEU P 517 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY P 522 " --> pdb=" O PRO P 518 " (cutoff:3.500A) Processing helix chain 'P' and resid 540 through 554 removed outlier: 3.658A pdb=" N ASN P 544 " --> pdb=" O SER P 540 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLN P 546 " --> pdb=" O ILE P 542 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU P 547 " --> pdb=" O MET P 543 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU P 548 " --> pdb=" O ASN P 544 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA P 549 " --> pdb=" O VAL P 545 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR P 550 " --> pdb=" O GLN P 546 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE P 551 " --> pdb=" O GLU P 547 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG P 552 " --> pdb=" O LEU P 548 " (cutoff:3.500A) Processing helix chain 'P' and resid 569 through 576 removed outlier: 4.102A pdb=" N GLN P 573 " --> pdb=" O GLY P 569 " (cutoff:3.500A) Processing helix chain 'P' and resid 602 through 605 No H-bonds generated for 'chain 'P' and resid 602 through 605' Processing helix chain 'P' and resid 618 through 628 removed outlier: 3.888A pdb=" N ARG P 622 " --> pdb=" O LYS P 618 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU P 623 " --> pdb=" O ALA P 619 " (cutoff:3.500A) Processing helix chain 'P' and resid 657 through 659 No H-bonds generated for 'chain 'P' and resid 657 through 659' Processing helix chain 'Q' and resid 99 through 110 removed outlier: 3.563A pdb=" N VAL Q 104 " --> pdb=" O ALA Q 100 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 130 Processing helix chain 'Q' and resid 144 through 156 removed outlier: 3.714A pdb=" N GLU Q 152 " --> pdb=" O VAL Q 148 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA Q 155 " --> pdb=" O ALA Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 184 removed outlier: 3.860A pdb=" N VAL Q 176 " --> pdb=" O ALA Q 172 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N SER Q 177 " --> pdb=" O THR Q 173 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY Q 178 " --> pdb=" O ASN Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 214 No H-bonds generated for 'chain 'Q' and resid 211 through 214' Processing helix chain 'Q' and resid 228 through 243 Proline residue: Q 232 - end of helix Processing helix chain 'Q' and resid 256 through 260 removed outlier: 3.545A pdb=" N GLN Q 260 " --> pdb=" O LYS Q 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 256 through 260' Processing helix chain 'Q' and resid 274 through 279 removed outlier: 3.882A pdb=" N ARG Q 279 " --> pdb=" O GLY Q 275 " (cutoff:3.500A) Processing helix chain 'Q' and resid 286 through 297 removed outlier: 3.836A pdb=" N GLN Q 291 " --> pdb=" O SER Q 287 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE Q 292 " --> pdb=" O HIS Q 288 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER Q 297 " --> pdb=" O VAL Q 293 " (cutoff:3.500A) Processing helix chain 'Q' and resid 308 through 312 removed outlier: 3.663A pdb=" N ASN Q 312 " --> pdb=" O GLY Q 309 " (cutoff:3.500A) Processing helix chain 'Q' and resid 316 through 323 removed outlier: 3.745A pdb=" N PHE Q 320 " --> pdb=" O GLU Q 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 355 through 362 removed outlier: 4.430A pdb=" N ALA Q 360 " --> pdb=" O TYR Q 356 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL Q 361 " --> pdb=" O ALA Q 357 " (cutoff:3.500A) Processing helix chain 'Q' and resid 376 through 379 No H-bonds generated for 'chain 'Q' and resid 376 through 379' Processing helix chain 'Q' and resid 415 through 428 removed outlier: 4.006A pdb=" N GLN Q 420 " --> pdb=" O LYS Q 416 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS Q 424 " --> pdb=" O GLN Q 420 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU Q 426 " --> pdb=" O MET Q 422 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN Q 428 " --> pdb=" O LYS Q 424 " (cutoff:3.500A) Processing helix chain 'Q' and resid 438 through 448 removed outlier: 3.649A pdb=" N LEU Q 444 " --> pdb=" O TRP Q 440 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN Q 447 " --> pdb=" O GLU Q 443 " (cutoff:3.500A) Processing helix chain 'Q' and resid 464 through 473 removed outlier: 3.896A pdb=" N ILE Q 468 " --> pdb=" O PRO Q 464 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU Q 473 " --> pdb=" O LYS Q 469 " (cutoff:3.500A) Processing helix chain 'Q' and resid 487 through 493 removed outlier: 4.027A pdb=" N ALA Q 492 " --> pdb=" O HIS Q 488 " (cutoff:3.500A) Processing helix chain 'Q' and resid 516 through 526 removed outlier: 3.633A pdb=" N ILE Q 521 " --> pdb=" O LEU Q 517 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL Q 525 " --> pdb=" O ILE Q 521 " (cutoff:3.500A) Processing helix chain 'Q' and resid 538 through 544 removed outlier: 4.479A pdb=" N ILE Q 542 " --> pdb=" O ASP Q 538 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN Q 544 " --> pdb=" O SER Q 540 " (cutoff:3.500A) Processing helix chain 'Q' and resid 546 through 552 removed outlier: 3.964A pdb=" N THR Q 550 " --> pdb=" O GLN Q 546 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG Q 552 " --> pdb=" O LEU Q 548 " (cutoff:3.500A) Processing helix chain 'Q' and resid 569 through 578 removed outlier: 3.561A pdb=" N ARG Q 577 " --> pdb=" O GLN Q 573 " (cutoff:3.500A) Processing helix chain 'Q' and resid 602 through 608 Processing helix chain 'Q' and resid 618 through 620 No H-bonds generated for 'chain 'Q' and resid 618 through 620' Processing helix chain 'Q' and resid 623 through 630 removed outlier: 3.556A pdb=" N LEU Q 629 " --> pdb=" O ILE Q 625 " (cutoff:3.500A) Processing helix chain 'Q' and resid 657 through 659 No H-bonds generated for 'chain 'Q' and resid 657 through 659' Processing helix chain 'R' and resid 99 through 108 removed outlier: 3.609A pdb=" N ALA R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 145 removed outlier: 3.706A pdb=" N GLU R 144 " --> pdb=" O GLN R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 188 removed outlier: 3.862A pdb=" N ALA R 181 " --> pdb=" O PRO R 177 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU R 182 " --> pdb=" O GLU R 178 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE R 183 " --> pdb=" O SER R 179 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N TRP R 185 " --> pdb=" O ALA R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 222 removed outlier: 4.218A pdb=" N LYS R 221 " --> pdb=" O GLU R 217 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS R 222 " --> pdb=" O ARG R 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 332 through 342 removed outlier: 3.652A pdb=" N VAL S 339 " --> pdb=" O ILE S 335 " (cutoff:3.500A) Processing helix chain 'S' and resid 371 through 383 removed outlier: 4.020A pdb=" N GLN S 379 " --> pdb=" O SER S 375 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLN S 380 " --> pdb=" O LYS S 376 " (cutoff:3.500A) Processing helix chain 'S' and resid 393 through 395 No H-bonds generated for 'chain 'S' and resid 393 through 395' Processing helix chain 'S' and resid 412 through 424 removed outlier: 3.544A pdb=" N ARG S 416 " --> pdb=" O ALA S 412 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP S 417 " --> pdb=" O ALA S 413 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP S 420 " --> pdb=" O ARG S 416 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ILE S 421 " --> pdb=" O ASP S 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 445 through 455 Processing sheet with id= A, first strand: chain 'A' and resid 115 through 117 removed outlier: 7.144A pdb=" N ILE A 163 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 194 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N HIS A 221 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASP A 253 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR A 223 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 328 through 330 removed outlier: 8.153A pdb=" N ALA A 329 " --> pdb=" O PRO A 302 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A 304 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A 366 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR A 305 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 368 " --> pdb=" O TYR A 305 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL A 392 " --> pdb=" O ALA A 369 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 480 through 482 Processing sheet with id= D, first strand: chain 'B' and resid 162 through 167 Processing sheet with id= E, first strand: chain 'B' and resid 328 through 330 removed outlier: 8.066A pdb=" N ALA B 329 " --> pdb=" O PRO B 302 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LEU B 304 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LEU B 366 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR B 305 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU B 368 " --> pdb=" O TYR B 305 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS B 390 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ALA B 369 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL B 392 " --> pdb=" O ALA B 369 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 533 through 537 removed outlier: 6.094A pdb=" N LYS B 559 " --> pdb=" O ASP B 534 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP B 536 " --> pdb=" O LYS B 559 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 561 " --> pdb=" O ASP B 536 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR B 635 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU B 562 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 637 " --> pdb=" O LEU B 562 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'F' and resid 152 through 157 removed outlier: 6.600A pdb=" N PHE F 92 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL F 155 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER F 90 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP F 157 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR F 88 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA F 126 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 206 through 208 removed outlier: 3.542A pdb=" N VAL F 229 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 172 through 174 removed outlier: 3.763A pdb=" N ASP F 196 " --> pdb=" O THR F 203 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 387 through 392 removed outlier: 6.875A pdb=" N LEU G 325 " --> pdb=" O HIS G 388 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL G 390 " --> pdb=" O SER G 323 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER G 323 " --> pdb=" O VAL G 390 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP G 392 " --> pdb=" O THR G 321 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR G 321 " --> pdb=" O ASP G 392 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 398 through 401 removed outlier: 3.621A pdb=" N LEU G 471 " --> pdb=" O SER G 399 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 437 through 441 removed outlier: 3.621A pdb=" N LEU G 441 " --> pdb=" O MET G 404 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 115 through 117 removed outlier: 7.146A pdb=" N ILE H 163 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY H 194 " --> pdb=" O ALA H 166 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS H 221 " --> pdb=" O LEU H 251 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASP H 253 " --> pdb=" O HIS H 221 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR H 223 " --> pdb=" O ASP H 253 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 328 through 330 removed outlier: 8.123A pdb=" N ALA H 329 " --> pdb=" O PRO H 302 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU H 304 " --> pdb=" O ALA H 329 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU H 366 " --> pdb=" O VAL H 303 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR H 305 " --> pdb=" O LEU H 366 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU H 368 " --> pdb=" O TYR H 305 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL H 392 " --> pdb=" O ALA H 369 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'H' and resid 480 through 482 Processing sheet with id= P, first strand: chain 'I' and resid 162 through 167 removed outlier: 6.625A pdb=" N HIS I 221 " --> pdb=" O LEU I 251 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ASP I 253 " --> pdb=" O HIS I 221 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR I 223 " --> pdb=" O ASP I 253 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 328 through 330 removed outlier: 8.062A pdb=" N ALA I 329 " --> pdb=" O PRO I 302 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU I 304 " --> pdb=" O ALA I 329 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU I 366 " --> pdb=" O VAL I 303 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR I 305 " --> pdb=" O LEU I 366 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU I 368 " --> pdb=" O TYR I 305 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS I 390 " --> pdb=" O LEU I 367 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ALA I 369 " --> pdb=" O LYS I 390 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL I 392 " --> pdb=" O ALA I 369 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'I' and resid 533 through 537 removed outlier: 6.072A pdb=" N LYS I 559 " --> pdb=" O ASP I 534 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASP I 536 " --> pdb=" O LYS I 559 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU I 561 " --> pdb=" O ASP I 536 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR I 635 " --> pdb=" O VAL I 560 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU I 562 " --> pdb=" O TYR I 635 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU I 637 " --> pdb=" O LEU I 562 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'J' and resid 152 through 157 removed outlier: 6.599A pdb=" N PHE J 92 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL J 155 " --> pdb=" O SER J 90 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER J 90 " --> pdb=" O VAL J 155 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASP J 157 " --> pdb=" O THR J 88 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR J 88 " --> pdb=" O ASP J 157 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA J 126 " --> pdb=" O VAL J 93 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 206 through 208 removed outlier: 3.542A pdb=" N VAL J 229 " --> pdb=" O LEU J 170 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 172 through 174 removed outlier: 3.764A pdb=" N ASP J 196 " --> pdb=" O THR J 203 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 387 through 392 removed outlier: 6.875A pdb=" N LEU K 325 " --> pdb=" O HIS K 388 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL K 390 " --> pdb=" O SER K 323 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER K 323 " --> pdb=" O VAL K 390 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP K 392 " --> pdb=" O THR K 321 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR K 321 " --> pdb=" O ASP K 392 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 398 through 401 removed outlier: 3.621A pdb=" N LEU K 471 " --> pdb=" O SER K 399 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 437 through 441 removed outlier: 3.621A pdb=" N LEU K 441 " --> pdb=" O MET K 404 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 115 through 117 removed outlier: 7.223A pdb=" N ILE L 163 " --> pdb=" O PHE L 116 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY L 194 " --> pdb=" O ALA L 166 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N HIS L 221 " --> pdb=" O LEU L 251 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ASP L 253 " --> pdb=" O HIS L 221 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR L 223 " --> pdb=" O ASP L 253 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 328 through 330 removed outlier: 8.121A pdb=" N ALA L 329 " --> pdb=" O PRO L 302 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU L 304 " --> pdb=" O ALA L 329 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU L 366 " --> pdb=" O VAL L 303 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR L 305 " --> pdb=" O LEU L 366 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU L 368 " --> pdb=" O TYR L 305 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL L 392 " --> pdb=" O ALA L 369 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'L' and resid 480 through 483 removed outlier: 6.516A pdb=" N TYR L 635 " --> pdb=" O VAL L 560 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU L 562 " --> pdb=" O TYR L 635 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU L 637 " --> pdb=" O LEU L 562 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASN L 564 " --> pdb=" O LEU L 637 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL L 639 " --> pdb=" O ASN L 564 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'M' and resid 189 through 195 removed outlier: 6.552A pdb=" N HIS M 221 " --> pdb=" O LEU M 251 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP M 253 " --> pdb=" O HIS M 221 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR M 223 " --> pdb=" O ASP M 253 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'M' and resid 302 through 306 removed outlier: 5.868A pdb=" N LEU M 366 " --> pdb=" O VAL M 303 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR M 305 " --> pdb=" O LEU M 366 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU M 368 " --> pdb=" O TYR M 305 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS M 390 " --> pdb=" O LEU M 367 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ALA M 369 " --> pdb=" O LYS M 390 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL M 392 " --> pdb=" O ALA M 369 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'M' and resid 533 through 537 removed outlier: 6.026A pdb=" N LYS M 559 " --> pdb=" O ASP M 534 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP M 536 " --> pdb=" O LYS M 559 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU M 561 " --> pdb=" O ASP M 536 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TYR M 635 " --> pdb=" O VAL M 560 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU M 562 " --> pdb=" O TYR M 635 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU M 637 " --> pdb=" O LEU M 562 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'N' and resid 152 through 157 removed outlier: 6.599A pdb=" N PHE N 92 " --> pdb=" O LEU N 153 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL N 155 " --> pdb=" O SER N 90 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER N 90 " --> pdb=" O VAL N 155 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP N 157 " --> pdb=" O THR N 88 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR N 88 " --> pdb=" O ASP N 157 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA N 126 " --> pdb=" O VAL N 93 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 206 through 208 removed outlier: 3.542A pdb=" N VAL N 229 " --> pdb=" O LEU N 170 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 172 through 174 removed outlier: 3.764A pdb=" N ASP N 196 " --> pdb=" O THR N 203 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'O' and resid 387 through 392 removed outlier: 6.875A pdb=" N LEU O 325 " --> pdb=" O HIS O 388 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL O 390 " --> pdb=" O SER O 323 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER O 323 " --> pdb=" O VAL O 390 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP O 392 " --> pdb=" O THR O 321 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR O 321 " --> pdb=" O ASP O 392 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'O' and resid 398 through 401 removed outlier: 3.621A pdb=" N LEU O 471 " --> pdb=" O SER O 399 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'O' and resid 437 through 441 removed outlier: 3.621A pdb=" N LEU O 441 " --> pdb=" O MET O 404 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'P' and resid 115 through 117 removed outlier: 7.144A pdb=" N ILE P 163 " --> pdb=" O PHE P 116 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY P 194 " --> pdb=" O ALA P 166 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N HIS P 221 " --> pdb=" O LEU P 251 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ASP P 253 " --> pdb=" O HIS P 221 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR P 223 " --> pdb=" O ASP P 253 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'P' and resid 328 through 330 removed outlier: 8.082A pdb=" N ALA P 329 " --> pdb=" O PRO P 302 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU P 304 " --> pdb=" O ALA P 329 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU P 366 " --> pdb=" O VAL P 303 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR P 305 " --> pdb=" O LEU P 366 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU P 368 " --> pdb=" O TYR P 305 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL P 392 " --> pdb=" O ALA P 369 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'P' and resid 480 through 482 Processing sheet with id= AN, first strand: chain 'Q' and resid 189 through 195 removed outlier: 6.483A pdb=" N HIS Q 221 " --> pdb=" O LEU Q 251 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ASP Q 253 " --> pdb=" O HIS Q 221 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR Q 223 " --> pdb=" O ASP Q 253 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'Q' and resid 302 through 306 removed outlier: 5.881A pdb=" N LEU Q 366 " --> pdb=" O VAL Q 303 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR Q 305 " --> pdb=" O LEU Q 366 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU Q 368 " --> pdb=" O TYR Q 305 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS Q 390 " --> pdb=" O LEU Q 367 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA Q 369 " --> pdb=" O LYS Q 390 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL Q 392 " --> pdb=" O ALA Q 369 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'Q' and resid 533 through 537 removed outlier: 6.077A pdb=" N LYS Q 559 " --> pdb=" O ASP Q 534 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASP Q 536 " --> pdb=" O LYS Q 559 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU Q 561 " --> pdb=" O ASP Q 536 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TYR Q 635 " --> pdb=" O VAL Q 560 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU Q 562 " --> pdb=" O TYR Q 635 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU Q 637 " --> pdb=" O LEU Q 562 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'R' and resid 152 through 157 removed outlier: 6.599A pdb=" N PHE R 92 " --> pdb=" O LEU R 153 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL R 155 " --> pdb=" O SER R 90 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER R 90 " --> pdb=" O VAL R 155 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP R 157 " --> pdb=" O THR R 88 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR R 88 " --> pdb=" O ASP R 157 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA R 126 " --> pdb=" O VAL R 93 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'R' and resid 206 through 208 removed outlier: 3.540A pdb=" N VAL R 229 " --> pdb=" O LEU R 170 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'R' and resid 172 through 174 removed outlier: 3.763A pdb=" N ASP R 196 " --> pdb=" O THR R 203 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'S' and resid 387 through 392 removed outlier: 6.875A pdb=" N LEU S 325 " --> pdb=" O HIS S 388 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL S 390 " --> pdb=" O SER S 323 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER S 323 " --> pdb=" O VAL S 390 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP S 392 " --> pdb=" O THR S 321 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR S 321 " --> pdb=" O ASP S 392 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'S' and resid 398 through 401 removed outlier: 3.620A pdb=" N LEU S 471 " --> pdb=" O SER S 399 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'S' and resid 437 through 441 removed outlier: 3.622A pdb=" N LEU S 441 " --> pdb=" O MET S 404 " (cutoff:3.500A) 1099 hydrogen bonds defined for protein. 3150 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.91 Time building geometry restraints manager: 21.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 7929 1.31 - 1.44: 11660 1.44 - 1.57: 27211 1.57 - 1.70: 84 1.70 - 1.83: 400 Bond restraints: 47284 Sorted by residual: bond pdb=" C5 TPP P 703 " pdb=" S1 TPP P 703 " ideal model delta sigma weight residual 1.727 1.571 0.156 1.00e-02 1.00e+04 2.42e+02 bond pdb=" C5 TPP A 703 " pdb=" S1 TPP A 703 " ideal model delta sigma weight residual 1.727 1.572 0.155 1.00e-02 1.00e+04 2.40e+02 bond pdb=" C5 TPP L 703 " pdb=" S1 TPP L 703 " ideal model delta sigma weight residual 1.727 1.574 0.153 1.00e-02 1.00e+04 2.34e+02 bond pdb=" C5 TPP H 703 " pdb=" S1 TPP H 703 " ideal model delta sigma weight residual 1.727 1.574 0.153 1.00e-02 1.00e+04 2.33e+02 bond pdb=" C5 TPP B 703 " pdb=" S1 TPP B 703 " ideal model delta sigma weight residual 1.727 1.582 0.145 1.00e-02 1.00e+04 2.12e+02 ... (remaining 47279 not shown) Histogram of bond angle deviations from ideal: 87.06 - 96.68: 8 96.68 - 106.31: 1728 106.31 - 115.94: 30098 115.94 - 125.57: 31695 125.57 - 135.19: 759 Bond angle restraints: 64288 Sorted by residual: angle pdb=" PA TPP Q 703 " pdb=" O3A TPP Q 703 " pdb=" PB TPP Q 703 " ideal model delta sigma weight residual 139.87 116.44 23.43 1.00e+00 1.00e+00 5.49e+02 angle pdb=" PA TPP I 703 " pdb=" O3A TPP I 703 " pdb=" PB TPP I 703 " ideal model delta sigma weight residual 139.87 116.52 23.35 1.00e+00 1.00e+00 5.45e+02 angle pdb=" PA TPP B 703 " pdb=" O3A TPP B 703 " pdb=" PB TPP B 703 " ideal model delta sigma weight residual 139.87 116.60 23.27 1.00e+00 1.00e+00 5.42e+02 angle pdb=" PA TPP M 703 " pdb=" O3A TPP M 703 " pdb=" PB TPP M 703 " ideal model delta sigma weight residual 139.87 116.72 23.15 1.00e+00 1.00e+00 5.36e+02 angle pdb=" PA TPP L 703 " pdb=" O3A TPP L 703 " pdb=" PB TPP L 703 " ideal model delta sigma weight residual 139.87 123.83 16.04 1.00e+00 1.00e+00 2.57e+02 ... (remaining 64283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 24925 17.97 - 35.94: 2998 35.94 - 53.91: 542 53.91 - 71.88: 148 71.88 - 89.85: 51 Dihedral angle restraints: 28664 sinusoidal: 11656 harmonic: 17008 Sorted by residual: dihedral pdb=" CA MET B 280 " pdb=" C MET B 280 " pdb=" N PRO B 281 " pdb=" CA PRO B 281 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA MET I 280 " pdb=" C MET I 280 " pdb=" N PRO I 281 " pdb=" CA PRO I 281 " ideal model delta harmonic sigma weight residual -180.00 -152.23 -27.77 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA MET M 280 " pdb=" C MET M 280 " pdb=" N PRO M 281 " pdb=" CA PRO M 281 " ideal model delta harmonic sigma weight residual -180.00 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 28661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 6280 0.093 - 0.185: 919 0.185 - 0.278: 86 0.278 - 0.370: 21 0.370 - 0.463: 10 Chirality restraints: 7316 Sorted by residual: chirality pdb=" CB ILE P 88 " pdb=" CA ILE P 88 " pdb=" CG1 ILE P 88 " pdb=" CG2 ILE P 88 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" C3B FAD P 702 " pdb=" C2B FAD P 702 " pdb=" C4B FAD P 702 " pdb=" O3B FAD P 702 " both_signs ideal model delta sigma weight residual False -2.72 -2.26 -0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" C3B FAD H 702 " pdb=" C2B FAD H 702 " pdb=" C4B FAD H 702 " pdb=" O3B FAD H 702 " both_signs ideal model delta sigma weight residual False -2.72 -2.26 -0.46 2.00e-01 2.50e+01 5.31e+00 ... (remaining 7313 not shown) Planarity restraints: 8328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 254 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO B 255 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO B 255 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 255 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 598 " 0.052 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO A 599 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 599 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 599 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 598 " 0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO H 599 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO H 599 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO H 599 " 0.041 5.00e-02 4.00e+02 ... (remaining 8325 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 1154 2.61 - 3.18: 42527 3.18 - 3.75: 86415 3.75 - 4.33: 117675 4.33 - 4.90: 180437 Nonbonded interactions: 428208 Sorted by model distance: nonbonded pdb=" OD1 ASP A 538 " pdb="MG MG A 701 " model vdw 2.034 2.170 nonbonded pdb=" OD1 ASP P 538 " pdb="MG MG P 701 " model vdw 2.042 2.170 nonbonded pdb="MG MG P 701 " pdb=" O2A TPP P 703 " model vdw 2.043 2.170 nonbonded pdb=" OD1 ASP L 538 " pdb="MG MG L 701 " model vdw 2.049 2.170 nonbonded pdb="MG MG A 701 " pdb=" O2A TPP A 703 " model vdw 2.052 2.170 ... (remaining 428203 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 86 through 207 or resid 209 through 667 or resid 701 throu \ gh 703)) selection = (chain 'B' and (resid 86 through 207 or resid 209 through 667 or resid 701 throu \ gh 703)) selection = (chain 'H' and (resid 86 through 207 or resid 209 through 667 or resid 701 throu \ gh 703)) selection = (chain 'I' and (resid 86 through 207 or resid 209 through 667 or resid 701 throu \ gh 703)) selection = (chain 'L' and (resid 86 through 207 or resid 209 through 667 or resid 701 throu \ gh 703)) selection = (chain 'M' and (resid 86 through 207 or resid 209 through 667 or resid 701 throu \ gh 703)) selection = (chain 'P' and (resid 86 through 207 or resid 209 through 667 or resid 701 throu \ gh 703)) selection = (chain 'Q' and (resid 86 through 207 or resid 209 through 667 or resid 701 throu \ gh 703)) } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.35 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: 4.830 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: 0.040 Extract box with map and model: 15.380 Check model and map are aligned: 0.730 Set scattering table: 0.410 Process input model: 148.400 Find NCS groups from input model: 3.550 Set up NCS constraints: 0.560 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.011 0.195 47284 Z= 0.715 Angle : 1.260 27.083 64288 Z= 0.676 Chirality : 0.068 0.463 7316 Planarity : 0.008 0.102 8328 Dihedral : 16.485 89.851 17728 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 0.16 % Allowed : 7.84 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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: -4.80 (0.09), residues: 5944 helix: -3.92 (0.07), residues: 1744 sheet: -3.37 (0.13), residues: 1020 loop : -2.66 (0.10), residues: 3180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP Q 574 HIS 0.022 0.002 HIS M 567 PHE 0.025 0.003 PHE Q 116 TYR 0.028 0.003 TYR H 356 ARG 0.011 0.001 ARG H 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1336 time to evaluate : 7.078 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 TYR cc_start: 0.8659 (t80) cc_final: 0.8428 (t80) REVERT: A 197 PRO cc_start: 0.8798 (Cg_exo) cc_final: 0.8406 (Cg_endo) REVERT: A 211 ILE cc_start: 0.9208 (tp) cc_final: 0.9008 (tp) REVERT: A 290 GLU cc_start: 0.8432 (tp30) cc_final: 0.8151 (tp30) REVERT: A 368 LEU cc_start: 0.7547 (tt) cc_final: 0.7000 (mp) REVERT: A 513 MET cc_start: 0.7890 (mtp) cc_final: 0.7500 (mtp) REVERT: A 623 GLU cc_start: 0.9091 (tp30) cc_final: 0.8365 (tm-30) REVERT: A 629 LEU cc_start: 0.8885 (mt) cc_final: 0.8656 (pt) REVERT: B 152 GLU cc_start: 0.6746 (tt0) cc_final: 0.5383 (tt0) REVERT: B 181 ASP cc_start: 0.8172 (t0) cc_final: 0.7847 (t70) REVERT: B 206 PHE cc_start: 0.5143 (t80) cc_final: 0.4570 (t80) REVERT: B 216 ARG cc_start: 0.8384 (ttm110) cc_final: 0.7983 (ttm-80) REVERT: B 333 MET cc_start: 0.8497 (mmm) cc_final: 0.8284 (mmm) REVERT: B 348 MET cc_start: 0.7442 (ttp) cc_final: 0.6960 (ppp) REVERT: B 488 HIS cc_start: 0.7792 (p-80) cc_final: 0.7436 (p-80) REVERT: B 572 MET cc_start: 0.4298 (tpt) cc_final: 0.3350 (tpt) REVERT: F 123 ARG cc_start: 0.6848 (mpt180) cc_final: 0.6609 (mmm160) REVERT: F 137 ARG cc_start: 0.7766 (tpt-90) cc_final: 0.7433 (tpm170) REVERT: F 140 GLN cc_start: 0.8639 (tp40) cc_final: 0.8411 (tp40) REVERT: F 148 LYS cc_start: 0.9126 (ttmt) cc_final: 0.8858 (ttmm) REVERT: F 172 LYS cc_start: 0.8949 (ttpt) cc_final: 0.8458 (ttmm) REVERT: F 221 LYS cc_start: 0.8979 (tptt) cc_final: 0.8607 (pttp) REVERT: G 345 TYR cc_start: 0.8105 (m-80) cc_final: 0.7867 (m-10) REVERT: G 389 GLU cc_start: 0.7955 (pp20) cc_final: 0.6144 (pp20) REVERT: G 391 HIS cc_start: 0.7017 (m170) cc_final: 0.6756 (m90) REVERT: G 400 GLU cc_start: 0.7800 (tm-30) cc_final: 0.6642 (tm-30) REVERT: G 462 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6471 (mm-30) REVERT: H 197 PRO cc_start: 0.8840 (Cg_exo) cc_final: 0.8219 (Cg_endo) REVERT: H 226 MET cc_start: 0.7493 (mmm) cc_final: 0.7288 (mmm) REVERT: H 239 PHE cc_start: 0.8291 (m-80) cc_final: 0.8091 (m-10) REVERT: H 290 GLU cc_start: 0.8447 (tp30) cc_final: 0.8173 (tp30) REVERT: H 333 MET cc_start: 0.6232 (mpp) cc_final: 0.5971 (mpp) REVERT: H 368 LEU cc_start: 0.7537 (tt) cc_final: 0.6808 (mp) REVERT: H 623 GLU cc_start: 0.9057 (tp30) cc_final: 0.8325 (tm-30) REVERT: H 629 LEU cc_start: 0.8846 (mt) cc_final: 0.8637 (pt) REVERT: I 103 LEU cc_start: 0.9093 (mt) cc_final: 0.8690 (mt) REVERT: I 174 ASN cc_start: 0.7874 (m-40) cc_final: 0.7430 (m-40) REVERT: I 206 PHE cc_start: 0.4870 (t80) cc_final: 0.4255 (t80) REVERT: I 216 ARG cc_start: 0.8335 (ttm110) cc_final: 0.8011 (ttm-80) REVERT: I 333 MET cc_start: 0.8432 (mmm) cc_final: 0.8207 (mmm) REVERT: I 348 MET cc_start: 0.7566 (ttp) cc_final: 0.7078 (ppp) REVERT: I 385 PHE cc_start: 0.7577 (t80) cc_final: 0.6582 (t80) REVERT: I 403 LYS cc_start: 0.8462 (tptt) cc_final: 0.8110 (tppt) REVERT: I 466 TYR cc_start: 0.7430 (t80) cc_final: 0.7039 (t80) REVERT: I 488 HIS cc_start: 0.7737 (p-80) cc_final: 0.7534 (p-80) REVERT: I 490 MET cc_start: 0.8984 (mmp) cc_final: 0.8533 (mmm) REVERT: I 558 VAL cc_start: 0.9402 (t) cc_final: 0.9158 (t) REVERT: I 572 MET cc_start: 0.4594 (tpt) cc_final: 0.3637 (tpt) REVERT: J 137 ARG cc_start: 0.7665 (tpt-90) cc_final: 0.7264 (tpm170) REVERT: J 140 GLN cc_start: 0.8619 (tp40) cc_final: 0.8370 (tp40) REVERT: J 141 GLN cc_start: 0.7772 (mt0) cc_final: 0.7283 (mt0) REVERT: J 172 LYS cc_start: 0.8945 (ttpt) cc_final: 0.8520 (ttmm) REVERT: J 221 LYS cc_start: 0.8988 (tptt) cc_final: 0.8578 (pttp) REVERT: K 345 TYR cc_start: 0.8165 (m-80) cc_final: 0.7932 (m-10) REVERT: K 389 GLU cc_start: 0.7973 (pp20) cc_final: 0.6130 (pp20) REVERT: K 391 HIS cc_start: 0.6960 (m170) cc_final: 0.6730 (m90) REVERT: K 400 GLU cc_start: 0.7758 (tm-30) cc_final: 0.6648 (tm-30) REVERT: K 462 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6468 (mm-30) REVERT: L 197 PRO cc_start: 0.8812 (Cg_exo) cc_final: 0.8078 (Cg_endo) REVERT: L 226 MET cc_start: 0.7459 (mmm) cc_final: 0.7256 (mmm) REVERT: L 290 GLU cc_start: 0.8450 (tp30) cc_final: 0.8171 (tp30) REVERT: L 368 LEU cc_start: 0.7540 (tt) cc_final: 0.6962 (mp) REVERT: L 623 GLU cc_start: 0.9036 (tp30) cc_final: 0.8311 (tm-30) REVERT: L 629 LEU cc_start: 0.8878 (mt) cc_final: 0.8649 (pt) REVERT: M 103 LEU cc_start: 0.8979 (mt) cc_final: 0.8653 (mt) REVERT: M 152 GLU cc_start: 0.6576 (mt-10) cc_final: 0.5120 (mt-10) REVERT: M 174 ASN cc_start: 0.7797 (m-40) cc_final: 0.7579 (m110) REVERT: M 181 ASP cc_start: 0.7470 (t0) cc_final: 0.7142 (t0) REVERT: M 206 PHE cc_start: 0.6187 (t80) cc_final: 0.5903 (t80) REVERT: M 216 ARG cc_start: 0.8373 (ttm110) cc_final: 0.8062 (ttm-80) REVERT: M 488 HIS cc_start: 0.7745 (p-80) cc_final: 0.7445 (p-80) REVERT: M 490 MET cc_start: 0.8967 (mmp) cc_final: 0.8157 (mmm) REVERT: M 513 MET cc_start: 0.8040 (mtp) cc_final: 0.7614 (mtp) REVERT: M 572 MET cc_start: 0.4454 (tpt) cc_final: 0.3385 (tpt) REVERT: M 579 TYR cc_start: 0.6206 (m-80) cc_final: 0.5944 (m-80) REVERT: N 172 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8436 (ttmm) REVERT: N 221 LYS cc_start: 0.9013 (tptt) cc_final: 0.8693 (pttp) REVERT: O 345 TYR cc_start: 0.8123 (m-80) cc_final: 0.7896 (m-10) REVERT: O 389 GLU cc_start: 0.7968 (pp20) cc_final: 0.6128 (pp20) REVERT: O 391 HIS cc_start: 0.7043 (m170) cc_final: 0.6758 (m90) REVERT: O 400 GLU cc_start: 0.7746 (tm-30) cc_final: 0.6629 (tm-30) REVERT: O 462 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6470 (mm-30) REVERT: P 118 TYR cc_start: 0.8680 (t80) cc_final: 0.8400 (t80) REVERT: P 197 PRO cc_start: 0.8806 (Cg_exo) cc_final: 0.7963 (Cg_endo) REVERT: P 200 MET cc_start: 0.8031 (mtp) cc_final: 0.7805 (mtp) REVERT: P 226 MET cc_start: 0.7518 (mmm) cc_final: 0.7289 (mmm) REVERT: P 290 GLU cc_start: 0.8471 (tp30) cc_final: 0.7492 (tp30) REVERT: P 294 ARG cc_start: 0.8162 (mtm180) cc_final: 0.7712 (mtm180) REVERT: P 623 GLU cc_start: 0.9046 (tp30) cc_final: 0.8333 (tm-30) REVERT: P 629 LEU cc_start: 0.8828 (mt) cc_final: 0.8598 (pt) REVERT: Q 103 LEU cc_start: 0.9241 (mt) cc_final: 0.8954 (mt) REVERT: Q 152 GLU cc_start: 0.6416 (mt-10) cc_final: 0.4976 (mt-10) REVERT: Q 181 ASP cc_start: 0.7740 (t0) cc_final: 0.7264 (t0) REVERT: Q 216 ARG cc_start: 0.8364 (ttm110) cc_final: 0.8013 (ttm-80) REVERT: Q 348 MET cc_start: 0.7606 (ttp) cc_final: 0.7343 (ppp) REVERT: Q 381 LYS cc_start: 0.7773 (tptm) cc_final: 0.7447 (tppt) REVERT: Q 488 HIS cc_start: 0.7799 (p-80) cc_final: 0.7543 (p-80) REVERT: Q 490 MET cc_start: 0.8901 (mmp) cc_final: 0.8395 (mmm) REVERT: Q 572 MET cc_start: 0.4019 (tpt) cc_final: 0.3031 (tpt) REVERT: R 137 ARG cc_start: 0.7709 (tpt-90) cc_final: 0.7302 (tpm170) REVERT: R 140 GLN cc_start: 0.8632 (tp40) cc_final: 0.8370 (tp40) REVERT: R 172 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8482 (ttmt) REVERT: R 221 LYS cc_start: 0.8954 (tptt) cc_final: 0.8591 (pttp) REVERT: S 345 TYR cc_start: 0.8137 (m-80) cc_final: 0.7887 (m-10) REVERT: S 389 GLU cc_start: 0.7970 (pp20) cc_final: 0.6161 (pp20) REVERT: S 391 HIS cc_start: 0.7008 (m170) cc_final: 0.6768 (m90) REVERT: S 400 GLU cc_start: 0.7784 (tm-30) cc_final: 0.6626 (tm-30) REVERT: S 462 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6487 (mm-30) outliers start: 8 outliers final: 0 residues processed: 1344 average time/residue: 0.5881 time to fit residues: 1283.7606 Evaluate side-chains 911 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 911 time to evaluate : 5.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 496 optimal weight: 3.9990 chunk 445 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 300 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 chunk 460 optimal weight: 0.3980 chunk 178 optimal weight: 3.9990 chunk 280 optimal weight: 0.7980 chunk 343 optimal weight: 2.9990 chunk 533 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN B 174 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN ** G 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 445 ASN ** I 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 643 HIS ** J 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 440 GLN ** K 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 261 GLN L 445 ASN ** M 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 ASN ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 440 GLN P 445 ASN P 487 GLN ** Q 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 566 GLN ** Q 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 440 GLN ** S 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 47284 Z= 0.274 Angle : 0.759 10.693 64288 Z= 0.382 Chirality : 0.048 0.266 7316 Planarity : 0.006 0.069 8328 Dihedral : 10.174 82.483 6824 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 29.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 1.97 % Allowed : 18.42 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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: -4.03 (0.10), residues: 5944 helix: -2.77 (0.09), residues: 1964 sheet: -2.98 (0.14), residues: 976 loop : -2.43 (0.11), residues: 3004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 504 HIS 0.007 0.001 HIS H 143 PHE 0.033 0.002 PHE M 240 TYR 0.036 0.002 TYR A 223 ARG 0.008 0.001 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1202 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1105 time to evaluate : 4.494 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: A 211 ILE cc_start: 0.9192 (tp) cc_final: 0.8968 (tp) REVERT: A 351 MET cc_start: 0.6711 (ttp) cc_final: 0.6508 (ttp) REVERT: A 368 LEU cc_start: 0.7581 (tt) cc_final: 0.7028 (mp) REVERT: A 504 TRP cc_start: 0.8002 (t-100) cc_final: 0.7545 (t-100) REVERT: A 513 MET cc_start: 0.8172 (mtp) cc_final: 0.7891 (mtt) REVERT: A 556 LEU cc_start: 0.8568 (mp) cc_final: 0.8294 (mp) REVERT: A 601 MET cc_start: 0.8154 (mmt) cc_final: 0.7678 (mmt) REVERT: A 604 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.8167 (t80) REVERT: A 623 GLU cc_start: 0.8777 (tp30) cc_final: 0.8317 (tm-30) REVERT: B 152 GLU cc_start: 0.7034 (tt0) cc_final: 0.5742 (tt0) REVERT: B 174 ASN cc_start: 0.7767 (m-40) cc_final: 0.6998 (m-40) REVERT: B 181 ASP cc_start: 0.7556 (t0) cc_final: 0.7145 (t0) REVERT: B 206 PHE cc_start: 0.5173 (t80) cc_final: 0.4490 (t80) REVERT: B 216 ARG cc_start: 0.8377 (ttm110) cc_final: 0.7927 (tpp80) REVERT: B 237 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7937 (mt-10) REVERT: B 300 LYS cc_start: 0.8249 (tttt) cc_final: 0.7637 (mmtm) REVERT: B 333 MET cc_start: 0.8578 (mmm) cc_final: 0.8371 (mmm) REVERT: B 348 MET cc_start: 0.7087 (ttp) cc_final: 0.6837 (ppp) REVERT: B 349 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7859 (pp) REVERT: B 381 LYS cc_start: 0.7940 (tptm) cc_final: 0.7538 (tppt) REVERT: B 490 MET cc_start: 0.8325 (mmm) cc_final: 0.7809 (mmm) REVERT: B 565 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7874 (p0) REVERT: B 628 MET cc_start: 0.8475 (tmm) cc_final: 0.8175 (tmm) REVERT: F 107 PHE cc_start: 0.8960 (m-80) cc_final: 0.8710 (m-10) REVERT: F 123 ARG cc_start: 0.6893 (mpt180) cc_final: 0.6497 (mmm160) REVERT: F 137 ARG cc_start: 0.7884 (tpt-90) cc_final: 0.7664 (tpm170) REVERT: F 140 GLN cc_start: 0.8579 (tp40) cc_final: 0.8329 (tp40) REVERT: F 141 GLN cc_start: 0.8072 (mt0) cc_final: 0.7856 (mt0) REVERT: F 172 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8390 (ttmt) REVERT: F 221 LYS cc_start: 0.8891 (tptt) cc_final: 0.8503 (pttp) REVERT: G 348 GLN cc_start: 0.7968 (tt0) cc_final: 0.7733 (tt0) REVERT: G 382 TYR cc_start: 0.8882 (m-10) cc_final: 0.8610 (m-80) REVERT: G 400 GLU cc_start: 0.7545 (tm-30) cc_final: 0.6376 (tm-30) REVERT: G 445 LEU cc_start: 0.8718 (tt) cc_final: 0.8283 (tp) REVERT: G 471 LEU cc_start: 0.8416 (mt) cc_final: 0.8209 (mt) REVERT: H 239 PHE cc_start: 0.8217 (m-80) cc_final: 0.7928 (m-10) REVERT: H 305 TYR cc_start: 0.7768 (t80) cc_final: 0.7244 (t80) REVERT: H 368 LEU cc_start: 0.7403 (tt) cc_final: 0.6831 (mp) REVERT: H 491 TRP cc_start: 0.7584 (m-10) cc_final: 0.7215 (m-10) REVERT: H 601 MET cc_start: 0.7994 (mmt) cc_final: 0.7599 (mmt) REVERT: H 623 GLU cc_start: 0.8721 (tp30) cc_final: 0.8285 (tm-30) REVERT: I 212 VAL cc_start: 0.9173 (m) cc_final: 0.8684 (m) REVERT: I 216 ARG cc_start: 0.8373 (ttm110) cc_final: 0.8082 (ttm-80) REVERT: I 300 LYS cc_start: 0.8269 (tttt) cc_final: 0.7618 (mmtm) REVERT: I 351 MET cc_start: 0.7698 (ttm) cc_final: 0.7490 (ttm) REVERT: I 385 PHE cc_start: 0.7557 (t80) cc_final: 0.6505 (t80) REVERT: I 466 TYR cc_start: 0.7492 (t80) cc_final: 0.7018 (t80) REVERT: I 490 MET cc_start: 0.8465 (mmp) cc_final: 0.7868 (mmm) REVERT: J 107 PHE cc_start: 0.8959 (m-80) cc_final: 0.8724 (m-10) REVERT: J 137 ARG cc_start: 0.7761 (tpt-90) cc_final: 0.7463 (tpm170) REVERT: J 167 GLU cc_start: 0.8026 (tt0) cc_final: 0.7681 (tt0) REVERT: J 172 LYS cc_start: 0.8805 (ttpt) cc_final: 0.8325 (ttmt) REVERT: J 196 ASP cc_start: 0.7723 (m-30) cc_final: 0.7477 (m-30) REVERT: J 221 LYS cc_start: 0.8882 (tptt) cc_final: 0.8581 (pttp) REVERT: K 382 TYR cc_start: 0.8803 (m-10) cc_final: 0.8561 (m-80) REVERT: K 400 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6383 (tm-30) REVERT: K 445 LEU cc_start: 0.8745 (tt) cc_final: 0.8289 (tp) REVERT: L 305 TYR cc_start: 0.7812 (t80) cc_final: 0.7366 (t80) REVERT: L 351 MET cc_start: 0.7388 (ttp) cc_final: 0.6670 (ttp) REVERT: L 368 LEU cc_start: 0.7603 (tt) cc_final: 0.7027 (mp) REVERT: L 543 MET cc_start: 0.8027 (mtp) cc_final: 0.7517 (mtm) REVERT: L 544 ASN cc_start: 0.8608 (t0) cc_final: 0.8394 (t0) REVERT: L 623 GLU cc_start: 0.8728 (tp30) cc_final: 0.8259 (tm-30) REVERT: M 206 PHE cc_start: 0.5722 (t80) cc_final: 0.4785 (t80) REVERT: M 216 ARG cc_start: 0.8321 (ttm110) cc_final: 0.8072 (ttm-80) REVERT: M 280 MET cc_start: 0.7399 (tpt) cc_final: 0.7187 (tpt) REVERT: M 300 LYS cc_start: 0.8363 (tttt) cc_final: 0.7773 (mmtt) REVERT: M 304 LEU cc_start: 0.8279 (tt) cc_final: 0.8035 (tt) REVERT: M 381 LYS cc_start: 0.7884 (tptm) cc_final: 0.7540 (tppt) REVERT: M 513 MET cc_start: 0.7888 (mtp) cc_final: 0.7350 (mtp) REVERT: M 536 ASP cc_start: 0.8056 (m-30) cc_final: 0.7607 (m-30) REVERT: M 565 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7780 (p0) REVERT: M 628 MET cc_start: 0.8480 (tmm) cc_final: 0.8169 (tmm) REVERT: N 161 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8477 (tp30) REVERT: N 167 GLU cc_start: 0.8102 (tt0) cc_final: 0.7726 (tt0) REVERT: N 172 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8300 (ttmt) REVERT: N 184 MET cc_start: 0.7245 (mtt) cc_final: 0.7043 (mtt) REVERT: N 221 LYS cc_start: 0.8921 (tptt) cc_final: 0.8576 (pttp) REVERT: O 382 TYR cc_start: 0.8789 (m-10) cc_final: 0.8540 (m-80) REVERT: O 400 GLU cc_start: 0.7492 (tm-30) cc_final: 0.6361 (tm-30) REVERT: O 445 LEU cc_start: 0.8695 (tt) cc_final: 0.8254 (tp) REVERT: P 197 PRO cc_start: 0.8846 (Cg_exo) cc_final: 0.8198 (Cg_endo) REVERT: P 200 MET cc_start: 0.7986 (mtp) cc_final: 0.7725 (mtp) REVERT: P 504 TRP cc_start: 0.8075 (t-100) cc_final: 0.7614 (t-100) REVERT: P 513 MET cc_start: 0.6395 (mtt) cc_final: 0.6154 (mtt) REVERT: P 601 MET cc_start: 0.7644 (mmt) cc_final: 0.7347 (mmt) REVERT: P 623 GLU cc_start: 0.8735 (tp30) cc_final: 0.8273 (tm-30) REVERT: Q 212 VAL cc_start: 0.9214 (m) cc_final: 0.8339 (m) REVERT: Q 216 ARG cc_start: 0.8393 (ttm110) cc_final: 0.7974 (tpp80) REVERT: Q 237 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7831 (mt-10) REVERT: Q 300 LYS cc_start: 0.8242 (tttt) cc_final: 0.7627 (mmtt) REVERT: Q 381 LYS cc_start: 0.7782 (tptm) cc_final: 0.7445 (tppt) REVERT: Q 488 HIS cc_start: 0.7855 (p-80) cc_final: 0.7649 (p-80) REVERT: Q 490 MET cc_start: 0.8320 (mmp) cc_final: 0.7968 (mmm) REVERT: R 137 ARG cc_start: 0.7850 (tpt-90) cc_final: 0.7523 (tpm170) REVERT: R 172 LYS cc_start: 0.8824 (ttpt) cc_final: 0.8381 (ttmt) REVERT: R 184 MET cc_start: 0.7314 (mtt) cc_final: 0.7073 (mtt) REVERT: R 221 LYS cc_start: 0.8860 (tptt) cc_final: 0.8489 (pttp) REVERT: S 382 TYR cc_start: 0.8799 (m-10) cc_final: 0.8552 (m-80) REVERT: S 400 GLU cc_start: 0.7546 (tm-30) cc_final: 0.6376 (tm-30) REVERT: S 445 LEU cc_start: 0.8734 (tt) cc_final: 0.8291 (tp) outliers start: 97 outliers final: 61 residues processed: 1151 average time/residue: 0.5807 time to fit residues: 1096.9595 Evaluate side-chains 972 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 907 time to evaluate : 5.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 641 CYS Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 122 ASN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain K residue 371 ASP Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 209 THR Chi-restraints excluded: chain M residue 359 TYR Chi-restraints excluded: chain M residue 507 SER Chi-restraints excluded: chain M residue 535 ILE Chi-restraints excluded: chain M residue 565 ASN Chi-restraints excluded: chain M residue 629 LEU Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain O residue 378 VAL Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 555 ASN Chi-restraints excluded: chain Q residue 359 TYR Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 219 ASN Chi-restraints excluded: chain S residue 339 VAL Chi-restraints excluded: chain S residue 352 VAL Chi-restraints excluded: chain S residue 371 ASP Chi-restraints excluded: chain S residue 378 VAL Chi-restraints excluded: chain S residue 418 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 296 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 444 optimal weight: 3.9990 chunk 363 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 534 optimal weight: 6.9990 chunk 577 optimal weight: 2.9990 chunk 476 optimal weight: 9.9990 chunk 530 optimal weight: 7.9990 chunk 182 optimal weight: 0.9980 chunk 429 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 HIS ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 452 GLN ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 ASN ** J 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 452 GLN L 404 ASN ** M 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 ASN ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 452 GLN ** Q 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 566 GLN ** Q 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 452 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 47284 Z= 0.296 Angle : 0.746 11.213 64288 Z= 0.374 Chirality : 0.048 0.264 7316 Planarity : 0.006 0.059 8328 Dihedral : 9.697 77.719 6824 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 30.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 2.56 % Allowed : 22.48 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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: -3.66 (0.10), residues: 5944 helix: -2.31 (0.10), residues: 1996 sheet: -2.83 (0.15), residues: 972 loop : -2.30 (0.11), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Q 504 HIS 0.017 0.001 HIS M 488 PHE 0.029 0.002 PHE B 240 TYR 0.020 0.002 TYR A 356 ARG 0.011 0.001 ARG Q 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1011 time to evaluate : 5.234 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 211 ILE cc_start: 0.9177 (tp) cc_final: 0.8948 (tp) REVERT: A 368 LEU cc_start: 0.7428 (tt) cc_final: 0.6989 (mp) REVERT: A 504 TRP cc_start: 0.8172 (t-100) cc_final: 0.7695 (t-100) REVERT: A 513 MET cc_start: 0.8173 (mtp) cc_final: 0.7882 (mtt) REVERT: A 568 LEU cc_start: 0.8832 (mm) cc_final: 0.8572 (mm) REVERT: A 601 MET cc_start: 0.8047 (mmt) cc_final: 0.7586 (mmt) REVERT: A 602 LEU cc_start: 0.9034 (mt) cc_final: 0.8701 (mt) REVERT: A 604 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8161 (t80) REVERT: A 623 GLU cc_start: 0.8812 (tp30) cc_final: 0.8289 (tm-30) REVERT: B 152 GLU cc_start: 0.7284 (tt0) cc_final: 0.6154 (tt0) REVERT: B 181 ASP cc_start: 0.7636 (t0) cc_final: 0.7202 (t0) REVERT: B 206 PHE cc_start: 0.5135 (t80) cc_final: 0.4439 (t80) REVERT: B 216 ARG cc_start: 0.8452 (ttm110) cc_final: 0.7952 (ttm-80) REVERT: B 234 ILE cc_start: 0.9285 (mm) cc_final: 0.8991 (mm) REVERT: B 237 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7716 (mt-10) REVERT: B 300 LYS cc_start: 0.8235 (tttt) cc_final: 0.7678 (mmtt) REVERT: B 348 MET cc_start: 0.7256 (ttp) cc_final: 0.6847 (ppp) REVERT: B 381 LYS cc_start: 0.7924 (tptm) cc_final: 0.7547 (tppt) REVERT: B 490 MET cc_start: 0.8249 (mmm) cc_final: 0.7820 (mmm) REVERT: B 628 MET cc_start: 0.8414 (tmm) cc_final: 0.8198 (tmm) REVERT: F 123 ARG cc_start: 0.6835 (mpt180) cc_final: 0.6450 (mmm160) REVERT: F 137 ARG cc_start: 0.7826 (tpt-90) cc_final: 0.7591 (tpm170) REVERT: F 140 GLN cc_start: 0.8686 (tp40) cc_final: 0.8459 (tp40) REVERT: F 172 LYS cc_start: 0.8851 (ttpt) cc_final: 0.8352 (ttmt) REVERT: F 221 LYS cc_start: 0.8886 (tptt) cc_final: 0.8508 (pttp) REVERT: G 348 GLN cc_start: 0.7913 (tt0) cc_final: 0.7689 (tt0) REVERT: G 382 TYR cc_start: 0.8945 (m-10) cc_final: 0.8668 (m-80) REVERT: G 400 GLU cc_start: 0.7589 (tm-30) cc_final: 0.6339 (tm-30) REVERT: G 402 GLU cc_start: 0.7653 (tt0) cc_final: 0.7269 (tt0) REVERT: G 445 LEU cc_start: 0.8549 (tt) cc_final: 0.8240 (tp) REVERT: G 471 LEU cc_start: 0.8448 (mt) cc_final: 0.8227 (mt) REVERT: H 216 ARG cc_start: 0.8205 (tpp80) cc_final: 0.7817 (tpp80) REVERT: H 290 GLU cc_start: 0.7926 (tp30) cc_final: 0.7691 (tp30) REVERT: H 305 TYR cc_start: 0.7863 (t80) cc_final: 0.7386 (t80) REVERT: H 368 LEU cc_start: 0.7357 (tt) cc_final: 0.6887 (mp) REVERT: H 491 TRP cc_start: 0.7582 (m-10) cc_final: 0.7078 (m-10) REVERT: H 513 MET cc_start: 0.6051 (mtp) cc_final: 0.5212 (mtt) REVERT: H 602 LEU cc_start: 0.8979 (mt) cc_final: 0.8599 (mt) REVERT: H 623 GLU cc_start: 0.8794 (tp30) cc_final: 0.8241 (tm-30) REVERT: I 181 ASP cc_start: 0.7416 (t0) cc_final: 0.7051 (t0) REVERT: I 216 ARG cc_start: 0.8144 (ttm110) cc_final: 0.7428 (ttm-80) REVERT: I 237 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7832 (mt-10) REVERT: I 300 LYS cc_start: 0.8248 (tttt) cc_final: 0.7652 (mmtt) REVERT: I 381 LYS cc_start: 0.7868 (tptm) cc_final: 0.7527 (tppt) REVERT: I 385 PHE cc_start: 0.7569 (t80) cc_final: 0.6484 (t80) REVERT: I 466 TYR cc_start: 0.7573 (t80) cc_final: 0.7078 (t80) REVERT: I 490 MET cc_start: 0.8342 (mmp) cc_final: 0.8068 (mmp) REVERT: I 544 ASN cc_start: 0.8533 (m110) cc_final: 0.8311 (m110) REVERT: J 172 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8362 (ttmt) REVERT: J 221 LYS cc_start: 0.8834 (tptt) cc_final: 0.8470 (pttp) REVERT: K 382 TYR cc_start: 0.8871 (m-10) cc_final: 0.8647 (m-80) REVERT: K 400 GLU cc_start: 0.7547 (tm-30) cc_final: 0.6375 (tm-30) REVERT: K 402 GLU cc_start: 0.7694 (tt0) cc_final: 0.7179 (tt0) REVERT: K 445 LEU cc_start: 0.8617 (tt) cc_final: 0.8339 (tp) REVERT: L 351 MET cc_start: 0.7443 (ttp) cc_final: 0.6789 (ttp) REVERT: L 368 LEU cc_start: 0.7487 (tt) cc_final: 0.7072 (mp) REVERT: L 568 LEU cc_start: 0.9010 (mm) cc_final: 0.8790 (mm) REVERT: L 602 LEU cc_start: 0.8756 (mt) cc_final: 0.8271 (mp) REVERT: L 623 GLU cc_start: 0.8820 (tp30) cc_final: 0.8235 (tm-30) REVERT: M 103 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8823 (mm) REVERT: M 152 GLU cc_start: 0.6319 (mt-10) cc_final: 0.4288 (mt-10) REVERT: M 181 ASP cc_start: 0.7384 (t0) cc_final: 0.6810 (t0) REVERT: M 206 PHE cc_start: 0.5490 (t80) cc_final: 0.4782 (t80) REVERT: M 216 ARG cc_start: 0.8046 (ttm110) cc_final: 0.6641 (ptp-110) REVERT: M 300 LYS cc_start: 0.8426 (tttt) cc_final: 0.7862 (mmtt) REVERT: M 304 LEU cc_start: 0.8152 (tt) cc_final: 0.7869 (tt) REVERT: M 381 LYS cc_start: 0.7881 (tptm) cc_final: 0.7519 (tppt) REVERT: M 490 MET cc_start: 0.8557 (mmp) cc_final: 0.7866 (mmm) REVERT: M 513 MET cc_start: 0.7938 (mtp) cc_final: 0.7350 (mtp) REVERT: M 536 ASP cc_start: 0.8233 (m-30) cc_final: 0.7637 (m-30) REVERT: M 628 MET cc_start: 0.8331 (tmm) cc_final: 0.8124 (tmm) REVERT: N 101 ASN cc_start: 0.8129 (t0) cc_final: 0.7851 (t0) REVERT: N 172 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8277 (ttmt) REVERT: N 221 LYS cc_start: 0.8871 (tptt) cc_final: 0.8519 (pttp) REVERT: O 382 TYR cc_start: 0.8810 (m-10) cc_final: 0.8581 (m-80) REVERT: O 400 GLU cc_start: 0.7558 (tm-30) cc_final: 0.6374 (tm-30) REVERT: O 402 GLU cc_start: 0.7674 (tt0) cc_final: 0.7319 (tt0) REVERT: O 445 LEU cc_start: 0.8549 (tt) cc_final: 0.8223 (tp) REVERT: P 197 PRO cc_start: 0.8827 (Cg_exo) cc_final: 0.8321 (Cg_endo) REVERT: P 200 MET cc_start: 0.7886 (mtp) cc_final: 0.7675 (mtp) REVERT: P 305 TYR cc_start: 0.7855 (t80) cc_final: 0.7389 (t80) REVERT: P 504 TRP cc_start: 0.8183 (t-100) cc_final: 0.7650 (t-100) REVERT: P 568 LEU cc_start: 0.8818 (mm) cc_final: 0.8608 (mm) REVERT: P 570 MET cc_start: 0.8220 (tpp) cc_final: 0.7900 (tpp) REVERT: P 601 MET cc_start: 0.7587 (mmt) cc_final: 0.7331 (mmt) REVERT: P 602 LEU cc_start: 0.9043 (mt) cc_final: 0.8666 (mt) REVERT: P 623 GLU cc_start: 0.8801 (tp30) cc_final: 0.8298 (tm-30) REVERT: Q 212 VAL cc_start: 0.9215 (m) cc_final: 0.8804 (m) REVERT: Q 216 ARG cc_start: 0.8454 (ttm110) cc_final: 0.8099 (ttm-80) REVERT: Q 237 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7805 (mt-10) REVERT: Q 300 LYS cc_start: 0.8276 (tttt) cc_final: 0.7638 (mmtm) REVERT: Q 381 LYS cc_start: 0.7777 (tptm) cc_final: 0.7440 (tppt) REVERT: Q 466 TYR cc_start: 0.6987 (t80) cc_final: 0.6638 (t80) REVERT: R 141 GLN cc_start: 0.7862 (mt0) cc_final: 0.7658 (mt0) REVERT: R 172 LYS cc_start: 0.8844 (ttpt) cc_final: 0.8346 (ttmt) REVERT: R 221 LYS cc_start: 0.8881 (tptt) cc_final: 0.8578 (pttp) REVERT: S 382 TYR cc_start: 0.8849 (m-10) cc_final: 0.8627 (m-80) REVERT: S 400 GLU cc_start: 0.7591 (tm-30) cc_final: 0.6368 (tm-30) REVERT: S 402 GLU cc_start: 0.7627 (tt0) cc_final: 0.7260 (tt0) REVERT: S 445 LEU cc_start: 0.8570 (tt) cc_final: 0.8244 (tp) outliers start: 126 outliers final: 90 residues processed: 1079 average time/residue: 0.5810 time to fit residues: 1037.0832 Evaluate side-chains 988 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 896 time to evaluate : 5.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 551 ILE Chi-restraints excluded: chain H residue 641 CYS Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 439 VAL Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 122 ASN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain K residue 371 ASP Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 418 VAL Chi-restraints excluded: chain K residue 441 LEU Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 218 ILE Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 292 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 177 SER Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 218 ILE Chi-restraints excluded: chain M residue 359 TYR Chi-restraints excluded: chain M residue 535 ILE Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain O residue 378 VAL Chi-restraints excluded: chain O residue 418 VAL Chi-restraints excluded: chain O residue 441 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 163 ILE Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 572 MET Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 359 TYR Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain S residue 352 VAL Chi-restraints excluded: chain S residue 371 ASP Chi-restraints excluded: chain S residue 378 VAL Chi-restraints excluded: chain S residue 418 VAL Chi-restraints excluded: chain S residue 441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 528 optimal weight: 2.9990 chunk 402 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 255 optimal weight: 5.9990 chunk 359 optimal weight: 6.9990 chunk 536 optimal weight: 0.7980 chunk 568 optimal weight: 0.0980 chunk 280 optimal weight: 0.3980 chunk 508 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN A 489 GLN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 391 HIS ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 GLN ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 ASN ** J 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 261 GLN ** M 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 ASN ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 489 GLN ** Q 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 566 GLN ** Q 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 47284 Z= 0.228 Angle : 0.706 11.295 64288 Z= 0.350 Chirality : 0.047 0.280 7316 Planarity : 0.005 0.062 8328 Dihedral : 9.334 75.988 6824 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 28.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.82 % Allowed : 23.98 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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: -3.38 (0.10), residues: 5944 helix: -1.98 (0.10), residues: 2036 sheet: -2.69 (0.15), residues: 936 loop : -2.22 (0.11), residues: 2972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 440 HIS 0.018 0.001 HIS Q 488 PHE 0.030 0.002 PHE H 385 TYR 0.023 0.002 TYR F 112 ARG 0.010 0.000 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1070 time to evaluate : 5.659 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: A 211 ILE cc_start: 0.9123 (tp) cc_final: 0.8905 (tp) REVERT: A 294 ARG cc_start: 0.8432 (ptm-80) cc_final: 0.7868 (mtm180) REVERT: A 504 TRP cc_start: 0.7938 (t-100) cc_final: 0.7521 (t-100) REVERT: A 568 LEU cc_start: 0.8863 (mm) cc_final: 0.8617 (mm) REVERT: A 601 MET cc_start: 0.7990 (mmt) cc_final: 0.7673 (mmt) REVERT: A 602 LEU cc_start: 0.8971 (mt) cc_final: 0.8597 (mt) REVERT: A 604 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8285 (t80) REVERT: A 623 GLU cc_start: 0.8782 (tp30) cc_final: 0.8253 (tm-30) REVERT: B 152 GLU cc_start: 0.6921 (tt0) cc_final: 0.5541 (tt0) REVERT: B 181 ASP cc_start: 0.7406 (t0) cc_final: 0.7059 (t0) REVERT: B 206 PHE cc_start: 0.4949 (t80) cc_final: 0.4352 (t80) REVERT: B 237 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7521 (mt-10) REVERT: B 272 ARG cc_start: 0.8331 (ttp-110) cc_final: 0.8106 (mtm110) REVERT: B 300 LYS cc_start: 0.8101 (tttt) cc_final: 0.7683 (mmtt) REVERT: B 381 LYS cc_start: 0.7869 (tptm) cc_final: 0.7529 (tppt) REVERT: B 490 MET cc_start: 0.8122 (mmm) cc_final: 0.7672 (mmm) REVERT: B 536 ASP cc_start: 0.8260 (m-30) cc_final: 0.7642 (m-30) REVERT: B 563 LEU cc_start: 0.8939 (tp) cc_final: 0.8730 (tp) REVERT: F 119 VAL cc_start: 0.9143 (p) cc_final: 0.8658 (m) REVERT: F 123 ARG cc_start: 0.6827 (mpt180) cc_final: 0.6409 (mmm160) REVERT: F 140 GLN cc_start: 0.8624 (tp40) cc_final: 0.8303 (tp40) REVERT: F 172 LYS cc_start: 0.8834 (ttpt) cc_final: 0.8306 (ttmt) REVERT: F 221 LYS cc_start: 0.8837 (tptt) cc_final: 0.8529 (pttp) REVERT: G 376 LYS cc_start: 0.9082 (tmtt) cc_final: 0.8678 (tmtt) REVERT: G 382 TYR cc_start: 0.8812 (m-10) cc_final: 0.8460 (m-80) REVERT: G 386 ASP cc_start: 0.8420 (m-30) cc_final: 0.8142 (m-30) REVERT: G 400 GLU cc_start: 0.7615 (tm-30) cc_final: 0.6426 (tm-30) REVERT: G 402 GLU cc_start: 0.7749 (tt0) cc_final: 0.7337 (tt0) REVERT: G 445 LEU cc_start: 0.8473 (tt) cc_final: 0.8193 (tp) REVERT: G 471 LEU cc_start: 0.8402 (mt) cc_final: 0.8199 (mt) REVERT: H 124 MET cc_start: 0.7858 (ptp) cc_final: 0.7630 (pmm) REVERT: H 216 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7811 (tpp80) REVERT: H 305 TYR cc_start: 0.7853 (t80) cc_final: 0.7374 (t80) REVERT: H 368 LEU cc_start: 0.7351 (tt) cc_final: 0.7137 (mp) REVERT: H 491 TRP cc_start: 0.7413 (m-10) cc_final: 0.6961 (m-10) REVERT: H 602 LEU cc_start: 0.8885 (mt) cc_final: 0.8462 (mt) REVERT: H 623 GLU cc_start: 0.8739 (tp30) cc_final: 0.8227 (tm-30) REVERT: I 103 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8810 (mm) REVERT: I 181 ASP cc_start: 0.7264 (t0) cc_final: 0.6865 (t0) REVERT: I 207 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7352 (mt0) REVERT: I 216 ARG cc_start: 0.8070 (ttm110) cc_final: 0.7069 (ttm110) REVERT: I 237 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7643 (mt-10) REVERT: I 300 LYS cc_start: 0.8121 (tttt) cc_final: 0.7677 (mmtt) REVERT: I 466 TYR cc_start: 0.7601 (t80) cc_final: 0.7031 (t80) REVERT: I 490 MET cc_start: 0.8258 (mmp) cc_final: 0.7750 (mmm) REVERT: I 544 ASN cc_start: 0.8638 (m110) cc_final: 0.8356 (m110) REVERT: J 172 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8292 (ttmt) REVERT: J 221 LYS cc_start: 0.8776 (tptt) cc_final: 0.8482 (pttp) REVERT: K 376 LYS cc_start: 0.9087 (tmtt) cc_final: 0.8635 (tmtt) REVERT: K 382 TYR cc_start: 0.8793 (m-10) cc_final: 0.8583 (m-80) REVERT: K 400 GLU cc_start: 0.7598 (tm-30) cc_final: 0.6400 (tm-30) REVERT: K 402 GLU cc_start: 0.7645 (tt0) cc_final: 0.7283 (tt0) REVERT: K 445 LEU cc_start: 0.8594 (tt) cc_final: 0.8227 (tp) REVERT: L 124 MET cc_start: 0.7869 (ptp) cc_final: 0.7659 (pmm) REVERT: L 181 ASP cc_start: 0.7915 (t0) cc_final: 0.7622 (t0) REVERT: L 351 MET cc_start: 0.7533 (ttp) cc_final: 0.6865 (ttp) REVERT: L 504 TRP cc_start: 0.8001 (t-100) cc_final: 0.7598 (t-100) REVERT: L 513 MET cc_start: 0.6344 (mtt) cc_final: 0.5420 (mtt) REVERT: L 544 ASN cc_start: 0.8238 (t0) cc_final: 0.8020 (t0) REVERT: L 570 MET cc_start: 0.8378 (tpp) cc_final: 0.8053 (tpp) REVERT: L 602 LEU cc_start: 0.8658 (mt) cc_final: 0.8117 (mp) REVERT: L 623 GLU cc_start: 0.8810 (tp30) cc_final: 0.8259 (tm-30) REVERT: M 103 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8805 (mm) REVERT: M 181 ASP cc_start: 0.7353 (t0) cc_final: 0.6892 (t0) REVERT: M 206 PHE cc_start: 0.5265 (t80) cc_final: 0.4558 (t80) REVERT: M 216 ARG cc_start: 0.8050 (ttm110) cc_final: 0.6577 (ptp-110) REVERT: M 300 LYS cc_start: 0.8199 (tttt) cc_final: 0.7780 (mmtt) REVERT: M 304 LEU cc_start: 0.8118 (tt) cc_final: 0.7841 (tt) REVERT: M 381 LYS cc_start: 0.7783 (tptm) cc_final: 0.7404 (mmmt) REVERT: M 466 TYR cc_start: 0.6892 (t80) cc_final: 0.6617 (t80) REVERT: M 490 MET cc_start: 0.8345 (mmp) cc_final: 0.7925 (mmm) REVERT: M 536 ASP cc_start: 0.8259 (m-30) cc_final: 0.7565 (m-30) REVERT: N 101 ASN cc_start: 0.8131 (t0) cc_final: 0.7853 (t0) REVERT: N 172 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8323 (ttmt) REVERT: N 221 LYS cc_start: 0.8872 (tptt) cc_final: 0.8536 (pttp) REVERT: O 376 LYS cc_start: 0.9000 (tmtt) cc_final: 0.8797 (tmtt) REVERT: O 382 TYR cc_start: 0.8732 (m-10) cc_final: 0.8525 (m-80) REVERT: O 400 GLU cc_start: 0.7576 (tm-30) cc_final: 0.6388 (tm-30) REVERT: O 402 GLU cc_start: 0.7776 (tt0) cc_final: 0.7425 (tt0) REVERT: O 445 LEU cc_start: 0.8470 (tt) cc_final: 0.8158 (tp) REVERT: P 197 PRO cc_start: 0.8709 (Cg_exo) cc_final: 0.8280 (Cg_endo) REVERT: P 504 TRP cc_start: 0.8000 (t-100) cc_final: 0.7542 (t-100) REVERT: P 601 MET cc_start: 0.7488 (mmt) cc_final: 0.7157 (mmt) REVERT: P 602 LEU cc_start: 0.8994 (mt) cc_final: 0.8580 (mt) REVERT: P 604 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8097 (t80) REVERT: P 623 GLU cc_start: 0.8750 (tp30) cc_final: 0.8179 (tm-30) REVERT: Q 103 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8878 (mm) REVERT: Q 181 ASP cc_start: 0.7370 (t0) cc_final: 0.6909 (t0) REVERT: Q 198 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7570 (ttm-80) REVERT: Q 206 PHE cc_start: 0.5343 (t80) cc_final: 0.4671 (t80) REVERT: Q 300 LYS cc_start: 0.8259 (tttt) cc_final: 0.7670 (mmtt) REVERT: Q 381 LYS cc_start: 0.7736 (tptm) cc_final: 0.7380 (tppt) REVERT: Q 466 TYR cc_start: 0.6945 (t80) cc_final: 0.6636 (t80) REVERT: Q 536 ASP cc_start: 0.8138 (m-30) cc_final: 0.7495 (m-30) REVERT: Q 554 GLU cc_start: 0.7609 (mp0) cc_final: 0.6007 (mm-30) REVERT: R 172 LYS cc_start: 0.8840 (ttpt) cc_final: 0.8312 (ttmt) REVERT: R 221 LYS cc_start: 0.8827 (tptt) cc_final: 0.8479 (pttp) REVERT: S 382 TYR cc_start: 0.8771 (m-10) cc_final: 0.8548 (m-80) REVERT: S 400 GLU cc_start: 0.7596 (tm-30) cc_final: 0.6402 (tm-30) REVERT: S 402 GLU cc_start: 0.7751 (tt0) cc_final: 0.7389 (tt0) REVERT: S 441 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8309 (pt) REVERT: S 445 LEU cc_start: 0.8500 (tt) cc_final: 0.8175 (tp) outliers start: 139 outliers final: 103 residues processed: 1146 average time/residue: 0.5822 time to fit residues: 1111.3756 Evaluate side-chains 1023 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 913 time to evaluate : 5.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 551 ILE Chi-restraints excluded: chain H residue 641 CYS Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 207 GLN Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 439 VAL Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 122 ASN Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain K residue 371 ASP Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 441 LEU Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 292 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 218 ILE Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain M residue 359 TYR Chi-restraints excluded: chain M residue 439 VAL Chi-restraints excluded: chain M residue 532 VAL Chi-restraints excluded: chain M residue 535 ILE Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 165 GLU Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain O residue 347 ILE Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain O residue 378 VAL Chi-restraints excluded: chain O residue 418 VAL Chi-restraints excluded: chain O residue 441 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 163 ILE Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 443 GLU Chi-restraints excluded: chain P residue 556 LEU Chi-restraints excluded: chain P residue 572 MET Chi-restraints excluded: chain P residue 604 PHE Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 218 ILE Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 306 VAL Chi-restraints excluded: chain Q residue 359 TYR Chi-restraints excluded: chain Q residue 439 VAL Chi-restraints excluded: chain Q residue 513 MET Chi-restraints excluded: chain Q residue 556 LEU Chi-restraints excluded: chain Q residue 637 LEU Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 ILE Chi-restraints excluded: chain S residue 347 ILE Chi-restraints excluded: chain S residue 352 VAL Chi-restraints excluded: chain S residue 371 ASP Chi-restraints excluded: chain S residue 378 VAL Chi-restraints excluded: chain S residue 441 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 473 optimal weight: 9.9990 chunk 322 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 423 optimal weight: 0.8980 chunk 234 optimal weight: 9.9990 chunk 485 optimal weight: 1.9990 chunk 392 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 290 optimal weight: 0.0060 chunk 510 optimal weight: 4.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 261 GLN ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 ASN ** J 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 ASN ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 494 GLN Q 566 GLN R 113 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 47284 Z= 0.240 Angle : 0.718 11.983 64288 Z= 0.355 Chirality : 0.047 0.272 7316 Planarity : 0.005 0.062 8328 Dihedral : 9.187 76.637 6824 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 28.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 3.37 % Allowed : 24.53 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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: -3.22 (0.10), residues: 5944 helix: -1.78 (0.10), residues: 2076 sheet: -2.63 (0.15), residues: 976 loop : -2.15 (0.11), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Q 504 HIS 0.012 0.001 HIS I 488 PHE 0.023 0.002 PHE I 385 TYR 0.028 0.002 TYR B 466 ARG 0.012 0.000 ARG I 272 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1016 time to evaluate : 6.063 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 199 ARG cc_start: 0.7678 (ptt90) cc_final: 0.7412 (mtm-85) REVERT: A 204 ASP cc_start: 0.6510 (t70) cc_final: 0.6253 (t70) REVERT: A 211 ILE cc_start: 0.9093 (tp) cc_final: 0.8891 (tp) REVERT: A 277 MET cc_start: 0.8228 (mmm) cc_final: 0.8024 (mmm) REVERT: A 429 ARG cc_start: 0.8241 (mtm-85) cc_final: 0.7882 (mtm-85) REVERT: A 504 TRP cc_start: 0.7954 (t-100) cc_final: 0.7522 (t-100) REVERT: A 513 MET cc_start: 0.7582 (mtp) cc_final: 0.7138 (mtt) REVERT: A 568 LEU cc_start: 0.8825 (mm) cc_final: 0.8583 (mm) REVERT: A 602 LEU cc_start: 0.8934 (mt) cc_final: 0.8515 (mt) REVERT: A 623 GLU cc_start: 0.8786 (tp30) cc_final: 0.8264 (tm-30) REVERT: B 152 GLU cc_start: 0.6942 (tt0) cc_final: 0.5567 (tt0) REVERT: B 181 ASP cc_start: 0.7375 (t0) cc_final: 0.7009 (t0) REVERT: B 300 LYS cc_start: 0.8029 (tttt) cc_final: 0.7631 (mmtt) REVERT: B 381 LYS cc_start: 0.7822 (tptm) cc_final: 0.7504 (tppt) REVERT: B 422 MET cc_start: 0.7602 (tpt) cc_final: 0.7213 (mmt) REVERT: B 490 MET cc_start: 0.8017 (mmm) cc_final: 0.7629 (mmm) REVERT: B 536 ASP cc_start: 0.8214 (m-30) cc_final: 0.7600 (m-30) REVERT: B 563 LEU cc_start: 0.9002 (tp) cc_final: 0.8767 (tp) REVERT: B 565 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.7882 (p0) REVERT: B 628 MET cc_start: 0.8692 (tmm) cc_final: 0.8172 (tmm) REVERT: F 113 ASN cc_start: 0.7977 (t0) cc_final: 0.7724 (t0) REVERT: F 123 ARG cc_start: 0.6872 (mpt180) cc_final: 0.6445 (mmm160) REVERT: F 140 GLN cc_start: 0.8600 (tp40) cc_final: 0.8335 (tp-100) REVERT: F 172 LYS cc_start: 0.8711 (ttpt) cc_final: 0.8223 (ttmt) REVERT: F 221 LYS cc_start: 0.8858 (tptt) cc_final: 0.8538 (pttp) REVERT: G 376 LYS cc_start: 0.8961 (tmtt) cc_final: 0.8652 (tmtt) REVERT: G 382 TYR cc_start: 0.8763 (m-10) cc_final: 0.8404 (m-80) REVERT: G 391 HIS cc_start: 0.6895 (m-70) cc_final: 0.6660 (m-70) REVERT: G 400 GLU cc_start: 0.7642 (tm-30) cc_final: 0.6476 (tm-30) REVERT: G 402 GLU cc_start: 0.7783 (tt0) cc_final: 0.7275 (tt0) REVERT: G 445 LEU cc_start: 0.8520 (tt) cc_final: 0.8251 (tp) REVERT: H 124 MET cc_start: 0.7785 (ptp) cc_final: 0.7548 (pmm) REVERT: H 216 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7764 (tpp80) REVERT: H 400 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7181 (tm-30) REVERT: H 491 TRP cc_start: 0.7408 (m-10) cc_final: 0.6928 (m-10) REVERT: H 602 LEU cc_start: 0.8814 (mt) cc_final: 0.8390 (mt) REVERT: H 623 GLU cc_start: 0.8750 (tp30) cc_final: 0.8236 (tm-30) REVERT: I 181 ASP cc_start: 0.7158 (t0) cc_final: 0.6896 (t0) REVERT: I 237 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7566 (mt-10) REVERT: I 300 LYS cc_start: 0.8071 (tttt) cc_final: 0.7644 (mmtt) REVERT: I 381 LYS cc_start: 0.7770 (tptm) cc_final: 0.7467 (mmmt) REVERT: I 466 TYR cc_start: 0.7640 (t80) cc_final: 0.7046 (t80) REVERT: I 490 MET cc_start: 0.8255 (mmp) cc_final: 0.7911 (mmm) REVERT: I 544 ASN cc_start: 0.8611 (m110) cc_final: 0.8313 (m110) REVERT: I 563 LEU cc_start: 0.8907 (tp) cc_final: 0.8591 (tp) REVERT: J 112 TYR cc_start: 0.6726 (m-10) cc_final: 0.5979 (m-10) REVERT: J 172 LYS cc_start: 0.8763 (ttpt) cc_final: 0.8290 (ttmt) REVERT: J 184 MET cc_start: 0.7116 (mtt) cc_final: 0.6844 (mtt) REVERT: J 221 LYS cc_start: 0.8851 (tptt) cc_final: 0.8513 (pttp) REVERT: K 345 TYR cc_start: 0.7657 (m-80) cc_final: 0.6763 (m-10) REVERT: K 376 LYS cc_start: 0.8934 (tmtt) cc_final: 0.8496 (tmtt) REVERT: K 382 TYR cc_start: 0.8785 (m-10) cc_final: 0.8564 (m-80) REVERT: K 400 GLU cc_start: 0.7589 (tm-30) cc_final: 0.6412 (tm-30) REVERT: K 402 GLU cc_start: 0.7677 (tt0) cc_final: 0.7445 (tt0) REVERT: K 445 LEU cc_start: 0.8589 (tt) cc_final: 0.8081 (tp) REVERT: L 124 MET cc_start: 0.7848 (ptp) cc_final: 0.7621 (pmm) REVERT: L 152 GLU cc_start: 0.8354 (tp30) cc_final: 0.8096 (tp30) REVERT: L 351 MET cc_start: 0.7484 (ttp) cc_final: 0.6872 (ttp) REVERT: L 504 TRP cc_start: 0.7929 (t-100) cc_final: 0.7576 (t-100) REVERT: L 513 MET cc_start: 0.6418 (mtt) cc_final: 0.5948 (mtt) REVERT: L 544 ASN cc_start: 0.8216 (t0) cc_final: 0.7930 (t0) REVERT: L 602 LEU cc_start: 0.8599 (mt) cc_final: 0.8024 (mp) REVERT: L 623 GLU cc_start: 0.8787 (tp30) cc_final: 0.8221 (tm-30) REVERT: M 103 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8831 (mm) REVERT: M 181 ASP cc_start: 0.7358 (t0) cc_final: 0.7012 (t0) REVERT: M 206 PHE cc_start: 0.4792 (t80) cc_final: 0.4325 (t80) REVERT: M 216 ARG cc_start: 0.8068 (ttm110) cc_final: 0.7508 (ptp-110) REVERT: M 300 LYS cc_start: 0.8070 (tttt) cc_final: 0.7768 (mmtt) REVERT: M 304 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7848 (tt) REVERT: M 381 LYS cc_start: 0.7751 (tptm) cc_final: 0.7387 (mmmt) REVERT: M 394 ILE cc_start: 0.8335 (pt) cc_final: 0.8079 (mm) REVERT: M 490 MET cc_start: 0.8610 (mmp) cc_final: 0.8170 (mmm) REVERT: M 536 ASP cc_start: 0.8222 (m-30) cc_final: 0.7469 (m-30) REVERT: M 628 MET cc_start: 0.8625 (tmm) cc_final: 0.8366 (tmm) REVERT: N 172 LYS cc_start: 0.8820 (ttpt) cc_final: 0.8316 (ttmt) REVERT: N 221 LYS cc_start: 0.8871 (tptt) cc_final: 0.8503 (pttp) REVERT: O 343 ARG cc_start: 0.7073 (mmm160) cc_final: 0.6816 (mmm160) REVERT: O 382 TYR cc_start: 0.8698 (m-10) cc_final: 0.8469 (m-80) REVERT: O 400 GLU cc_start: 0.7570 (tm-30) cc_final: 0.6407 (tm-30) REVERT: O 402 GLU cc_start: 0.7777 (tt0) cc_final: 0.7547 (tt0) REVERT: O 445 LEU cc_start: 0.8509 (tt) cc_final: 0.8053 (tp) REVERT: P 277 MET cc_start: 0.8307 (mmm) cc_final: 0.8025 (mmm) REVERT: P 400 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7209 (tm-30) REVERT: P 504 TRP cc_start: 0.8079 (t-100) cc_final: 0.7543 (t-100) REVERT: P 536 ASP cc_start: 0.7488 (m-30) cc_final: 0.7237 (m-30) REVERT: P 601 MET cc_start: 0.7445 (mmt) cc_final: 0.7206 (mmt) REVERT: P 602 LEU cc_start: 0.8959 (mt) cc_final: 0.8548 (mt) REVERT: P 604 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8217 (t80) REVERT: P 623 GLU cc_start: 0.8757 (tp30) cc_final: 0.8196 (tm-30) REVERT: Q 103 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8865 (mm) REVERT: Q 152 GLU cc_start: 0.6600 (mt-10) cc_final: 0.4294 (mt-10) REVERT: Q 181 ASP cc_start: 0.7305 (t0) cc_final: 0.6708 (t0) REVERT: Q 206 PHE cc_start: 0.5140 (t80) cc_final: 0.4491 (t80) REVERT: Q 300 LYS cc_start: 0.8212 (tttt) cc_final: 0.7638 (mmtt) REVERT: Q 381 LYS cc_start: 0.7718 (tptm) cc_final: 0.7365 (tppt) REVERT: Q 466 TYR cc_start: 0.6933 (t80) cc_final: 0.6671 (t80) REVERT: Q 536 ASP cc_start: 0.8087 (m-30) cc_final: 0.7372 (m-30) REVERT: Q 554 GLU cc_start: 0.7432 (mp0) cc_final: 0.5899 (mm-30) REVERT: R 163 GLN cc_start: 0.8568 (pt0) cc_final: 0.8340 (pt0) REVERT: R 172 LYS cc_start: 0.8792 (ttpt) cc_final: 0.8311 (ttmt) REVERT: R 221 LYS cc_start: 0.8852 (tptt) cc_final: 0.8481 (pttp) REVERT: S 382 TYR cc_start: 0.8753 (m-10) cc_final: 0.8527 (m-80) REVERT: S 400 GLU cc_start: 0.7611 (tm-30) cc_final: 0.6340 (tm-30) REVERT: S 402 GLU cc_start: 0.7769 (tt0) cc_final: 0.7369 (tt0) REVERT: S 445 LEU cc_start: 0.8529 (tt) cc_final: 0.8212 (tp) REVERT: S 447 LYS cc_start: 0.5818 (mmtt) cc_final: 0.5519 (mmtm) outliers start: 166 outliers final: 124 residues processed: 1117 average time/residue: 0.5774 time to fit residues: 1067.9619 Evaluate side-chains 1052 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 923 time to evaluate : 5.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 261 GLN Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 551 ILE Chi-restraints excluded: chain H residue 641 CYS Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 439 VAL Chi-restraints excluded: chain I residue 532 VAL Chi-restraints excluded: chain I residue 535 ILE Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain I residue 620 ASP Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 122 ASN Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain K residue 371 ASP Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 441 LEU Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 218 ILE Chi-restraints excluded: chain L residue 292 ILE Chi-restraints excluded: chain L residue 641 CYS Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 218 ILE Chi-restraints excluded: chain M residue 243 THR Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain M residue 359 TYR Chi-restraints excluded: chain M residue 439 VAL Chi-restraints excluded: chain M residue 532 VAL Chi-restraints excluded: chain M residue 535 ILE Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 556 LEU Chi-restraints excluded: chain M residue 629 LEU Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 165 GLU Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 347 ILE Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain O residue 378 VAL Chi-restraints excluded: chain O residue 420 ASP Chi-restraints excluded: chain O residue 441 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 163 ILE Chi-restraints excluded: chain P residue 200 MET Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 231 ILE Chi-restraints excluded: chain P residue 443 GLU Chi-restraints excluded: chain P residue 572 MET Chi-restraints excluded: chain P residue 604 PHE Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 306 VAL Chi-restraints excluded: chain Q residue 359 TYR Chi-restraints excluded: chain Q residue 439 VAL Chi-restraints excluded: chain Q residue 513 MET Chi-restraints excluded: chain Q residue 532 VAL Chi-restraints excluded: chain Q residue 535 ILE Chi-restraints excluded: chain Q residue 556 LEU Chi-restraints excluded: chain Q residue 571 VAL Chi-restraints excluded: chain Q residue 637 LEU Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain S residue 308 LEU Chi-restraints excluded: chain S residue 347 ILE Chi-restraints excluded: chain S residue 352 VAL Chi-restraints excluded: chain S residue 371 ASP Chi-restraints excluded: chain S residue 378 VAL Chi-restraints excluded: chain S residue 441 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 191 optimal weight: 0.2980 chunk 511 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 333 optimal weight: 0.1980 chunk 140 optimal weight: 2.9990 chunk 568 optimal weight: 0.0870 chunk 472 optimal weight: 7.9990 chunk 263 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 261 GLN I 207 GLN ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 122 ASN ** K 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 494 GLN ** M 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 380 GLN ** P 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 47284 Z= 0.216 Angle : 0.714 11.951 64288 Z= 0.349 Chirality : 0.047 0.250 7316 Planarity : 0.005 0.058 8328 Dihedral : 8.979 77.770 6824 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 28.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.27 % Allowed : 25.28 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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: -3.04 (0.10), residues: 5944 helix: -1.59 (0.11), residues: 2020 sheet: -2.63 (0.15), residues: 1012 loop : -2.02 (0.11), residues: 2912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP I 491 HIS 0.010 0.001 HIS M 488 PHE 0.027 0.002 PHE A 385 TYR 0.024 0.002 TYR M 466 ARG 0.014 0.001 ARG M 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1039 time to evaluate : 6.019 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: A 204 ASP cc_start: 0.6410 (t70) cc_final: 0.6203 (t70) REVERT: A 216 ARG cc_start: 0.7950 (tpp80) cc_final: 0.7508 (tpp80) REVERT: A 294 ARG cc_start: 0.8401 (ptm-80) cc_final: 0.7757 (mtm180) REVERT: A 305 TYR cc_start: 0.7910 (t80) cc_final: 0.7389 (t80) REVERT: A 351 MET cc_start: 0.7262 (ttp) cc_final: 0.7021 (ttp) REVERT: A 429 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.7861 (mtm-85) REVERT: A 504 TRP cc_start: 0.7892 (t-100) cc_final: 0.7535 (t-100) REVERT: A 513 MET cc_start: 0.7667 (mtp) cc_final: 0.7327 (mtt) REVERT: A 544 ASN cc_start: 0.8491 (t0) cc_final: 0.8172 (t0) REVERT: A 568 LEU cc_start: 0.8694 (mm) cc_final: 0.8487 (mm) REVERT: A 602 LEU cc_start: 0.8782 (mt) cc_final: 0.8393 (mt) REVERT: A 623 GLU cc_start: 0.8733 (tp30) cc_final: 0.8236 (tm-30) REVERT: B 181 ASP cc_start: 0.7204 (t0) cc_final: 0.6713 (t0) REVERT: B 206 PHE cc_start: 0.4629 (t80) cc_final: 0.4111 (t80) REVERT: B 216 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7807 (ttm-80) REVERT: B 300 LYS cc_start: 0.8051 (tttt) cc_final: 0.7681 (mmtt) REVERT: B 381 LYS cc_start: 0.7780 (tptm) cc_final: 0.7433 (tppt) REVERT: B 422 MET cc_start: 0.7555 (tpt) cc_final: 0.7120 (mmt) REVERT: B 536 ASP cc_start: 0.8126 (m-30) cc_final: 0.7490 (m-30) REVERT: B 544 ASN cc_start: 0.8264 (m-40) cc_final: 0.7919 (m110) REVERT: B 563 LEU cc_start: 0.9019 (tp) cc_final: 0.8806 (tp) REVERT: B 628 MET cc_start: 0.8413 (tmm) cc_final: 0.8170 (tmm) REVERT: B 629 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8102 (tp) REVERT: F 123 ARG cc_start: 0.6835 (mpt180) cc_final: 0.6445 (mmm160) REVERT: F 140 GLN cc_start: 0.8562 (tp40) cc_final: 0.8339 (tp-100) REVERT: F 172 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8282 (ttmt) REVERT: F 221 LYS cc_start: 0.8817 (tptt) cc_final: 0.8487 (pttp) REVERT: F 222 LYS cc_start: 0.8690 (ptmt) cc_final: 0.8236 (pttt) REVERT: G 314 THR cc_start: 0.7058 (OUTLIER) cc_final: 0.6803 (p) REVERT: G 345 TYR cc_start: 0.7502 (m-80) cc_final: 0.6721 (m-10) REVERT: G 376 LYS cc_start: 0.8985 (tmtt) cc_final: 0.8740 (tmtt) REVERT: G 382 TYR cc_start: 0.8719 (m-10) cc_final: 0.8351 (m-80) REVERT: G 400 GLU cc_start: 0.7626 (tm-30) cc_final: 0.6507 (tm-30) REVERT: G 402 GLU cc_start: 0.7792 (tt0) cc_final: 0.7545 (tt0) REVERT: G 445 LEU cc_start: 0.8526 (tt) cc_final: 0.7923 (tp) REVERT: G 471 LEU cc_start: 0.8319 (mt) cc_final: 0.8062 (mt) REVERT: H 124 MET cc_start: 0.7756 (ptp) cc_final: 0.7542 (pmm) REVERT: H 400 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7178 (tm-30) REVERT: H 513 MET cc_start: 0.5921 (mtp) cc_final: 0.5615 (mtt) REVERT: H 536 ASP cc_start: 0.7219 (m-30) cc_final: 0.6951 (m-30) REVERT: H 623 GLU cc_start: 0.8672 (tp30) cc_final: 0.8197 (tm-30) REVERT: I 103 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8789 (mm) REVERT: I 181 ASP cc_start: 0.7078 (t0) cc_final: 0.6720 (t0) REVERT: I 206 PHE cc_start: 0.4715 (t80) cc_final: 0.4208 (t80) REVERT: I 216 ARG cc_start: 0.7706 (ttm110) cc_final: 0.7380 (ttm110) REVERT: I 300 LYS cc_start: 0.8068 (tttt) cc_final: 0.7665 (mmtt) REVERT: I 381 LYS cc_start: 0.7742 (tptm) cc_final: 0.7429 (mmmt) REVERT: I 466 TYR cc_start: 0.7585 (t80) cc_final: 0.6997 (t80) REVERT: I 490 MET cc_start: 0.7891 (mmp) cc_final: 0.7664 (mmm) REVERT: I 554 GLU cc_start: 0.7428 (mp0) cc_final: 0.5952 (mm-30) REVERT: I 563 LEU cc_start: 0.8858 (tp) cc_final: 0.8611 (tp) REVERT: I 628 MET cc_start: 0.7404 (mtt) cc_final: 0.7193 (mtt) REVERT: J 172 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8281 (ttmt) REVERT: J 205 GLU cc_start: 0.7288 (tt0) cc_final: 0.6594 (tm-30) REVERT: J 221 LYS cc_start: 0.8766 (tptt) cc_final: 0.8410 (pttp) REVERT: K 345 TYR cc_start: 0.7317 (m-80) cc_final: 0.6767 (m-10) REVERT: K 382 TYR cc_start: 0.8662 (m-10) cc_final: 0.8420 (m-80) REVERT: K 400 GLU cc_start: 0.7594 (tm-30) cc_final: 0.6299 (tm-30) REVERT: K 445 LEU cc_start: 0.8543 (tt) cc_final: 0.8103 (tp) REVERT: L 216 ARG cc_start: 0.8444 (tpp80) cc_final: 0.8222 (tpp80) REVERT: L 333 MET cc_start: 0.6515 (mpp) cc_final: 0.5808 (mpp) REVERT: L 400 GLU cc_start: 0.7322 (tm-30) cc_final: 0.7028 (tm-30) REVERT: L 504 TRP cc_start: 0.7792 (t-100) cc_final: 0.7562 (t-100) REVERT: L 513 MET cc_start: 0.6341 (mtt) cc_final: 0.5929 (mtt) REVERT: L 570 MET cc_start: 0.7764 (tmm) cc_final: 0.7185 (tmm) REVERT: L 602 LEU cc_start: 0.8515 (mt) cc_final: 0.7951 (mp) REVERT: L 623 GLU cc_start: 0.8733 (tp30) cc_final: 0.8206 (tm-30) REVERT: M 103 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8759 (mm) REVERT: M 152 GLU cc_start: 0.6844 (mt-10) cc_final: 0.5182 (mt-10) REVERT: M 181 ASP cc_start: 0.7156 (t0) cc_final: 0.6526 (t0) REVERT: M 206 PHE cc_start: 0.4286 (t80) cc_final: 0.3965 (t80) REVERT: M 216 ARG cc_start: 0.7967 (ttm110) cc_final: 0.7371 (ptp-110) REVERT: M 272 ARG cc_start: 0.8148 (ttp-110) cc_final: 0.7797 (ptp-170) REVERT: M 300 LYS cc_start: 0.8054 (tttt) cc_final: 0.7782 (mmtt) REVERT: M 347 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.6702 (t70) REVERT: M 381 LYS cc_start: 0.7721 (tptm) cc_final: 0.7350 (mmmt) REVERT: M 536 ASP cc_start: 0.8195 (m-30) cc_final: 0.7498 (m-30) REVERT: M 561 LEU cc_start: 0.8931 (tt) cc_final: 0.8663 (tp) REVERT: M 628 MET cc_start: 0.8472 (tmm) cc_final: 0.8215 (tmm) REVERT: M 629 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8003 (tp) REVERT: N 172 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8184 (ttmt) REVERT: N 221 LYS cc_start: 0.8778 (tptt) cc_final: 0.8424 (pttp) REVERT: O 320 HIS cc_start: 0.8293 (m90) cc_final: 0.8076 (m-70) REVERT: O 382 TYR cc_start: 0.8623 (m-10) cc_final: 0.8355 (m-80) REVERT: O 400 GLU cc_start: 0.7477 (tm-30) cc_final: 0.6318 (tm-30) REVERT: O 402 GLU cc_start: 0.7779 (tt0) cc_final: 0.7341 (tt0) REVERT: O 441 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7820 (pt) REVERT: O 445 LEU cc_start: 0.8454 (tt) cc_final: 0.8154 (tp) REVERT: O 447 LYS cc_start: 0.5596 (mmtt) cc_final: 0.5324 (mmtm) REVERT: P 333 MET cc_start: 0.6741 (mpp) cc_final: 0.5645 (mpp) REVERT: P 400 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7128 (tm-30) REVERT: P 489 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7775 (tp40) REVERT: P 504 TRP cc_start: 0.7943 (t-100) cc_final: 0.7375 (t-100) REVERT: P 505 LEU cc_start: 0.7821 (mm) cc_final: 0.7541 (mm) REVERT: P 561 LEU cc_start: 0.8662 (mt) cc_final: 0.8059 (mp) REVERT: P 570 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7182 (tmm) REVERT: P 601 MET cc_start: 0.7279 (mmt) cc_final: 0.7071 (mmt) REVERT: P 604 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.8133 (t80) REVERT: P 623 GLU cc_start: 0.8712 (tp30) cc_final: 0.8207 (tm-30) REVERT: Q 103 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8868 (mm) REVERT: Q 152 GLU cc_start: 0.6621 (mt-10) cc_final: 0.6221 (mt-10) REVERT: Q 206 PHE cc_start: 0.4827 (t80) cc_final: 0.4258 (t80) REVERT: Q 216 ARG cc_start: 0.7970 (ttm-80) cc_final: 0.6756 (ttm110) REVERT: Q 300 LYS cc_start: 0.8070 (tttt) cc_final: 0.7639 (mmtt) REVERT: Q 381 LYS cc_start: 0.7682 (tptm) cc_final: 0.7303 (mmmt) REVERT: Q 536 ASP cc_start: 0.7953 (m-30) cc_final: 0.7183 (m-30) REVERT: Q 554 GLU cc_start: 0.7267 (mp0) cc_final: 0.5822 (mm-30) REVERT: Q 563 LEU cc_start: 0.8975 (tp) cc_final: 0.8774 (tp) REVERT: R 101 ASN cc_start: 0.8215 (t0) cc_final: 0.8004 (t0) REVERT: R 113 ASN cc_start: 0.8035 (t0) cc_final: 0.7773 (t0) REVERT: R 172 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8284 (ttmt) REVERT: R 184 MET cc_start: 0.7171 (mtt) cc_final: 0.6878 (mtt) REVERT: R 221 LYS cc_start: 0.8810 (tptt) cc_final: 0.8433 (pttp) REVERT: S 320 HIS cc_start: 0.8280 (m90) cc_final: 0.8076 (m-70) REVERT: S 382 TYR cc_start: 0.8716 (m-10) cc_final: 0.8435 (m-80) REVERT: S 400 GLU cc_start: 0.7614 (tm-30) cc_final: 0.6363 (tm-30) REVERT: S 402 GLU cc_start: 0.7826 (tt0) cc_final: 0.7409 (tt0) REVERT: S 445 LEU cc_start: 0.8498 (tt) cc_final: 0.8185 (tp) REVERT: S 447 LYS cc_start: 0.5585 (mmtt) cc_final: 0.5320 (mmtm) outliers start: 161 outliers final: 117 residues processed: 1139 average time/residue: 0.5731 time to fit residues: 1081.6450 Evaluate side-chains 1076 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 948 time to evaluate : 5.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 261 GLN Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 457 THR Chi-restraints excluded: chain H residue 641 CYS Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 397 ASP Chi-restraints excluded: chain I residue 439 VAL Chi-restraints excluded: chain I residue 532 VAL Chi-restraints excluded: chain I residue 535 ILE Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain I residue 620 ASP Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 122 ASN Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain K residue 371 ASP Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 441 LEU Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 209 THR Chi-restraints excluded: chain L residue 218 ILE Chi-restraints excluded: chain L residue 292 ILE Chi-restraints excluded: chain L residue 457 THR Chi-restraints excluded: chain L residue 641 CYS Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 218 ILE Chi-restraints excluded: chain M residue 347 HIS Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain M residue 359 TYR Chi-restraints excluded: chain M residue 439 VAL Chi-restraints excluded: chain M residue 532 VAL Chi-restraints excluded: chain M residue 535 ILE Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 556 LEU Chi-restraints excluded: chain M residue 629 LEU Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 PHE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 165 GLU Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 347 ILE Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain O residue 378 VAL Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain O residue 441 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 231 ILE Chi-restraints excluded: chain P residue 457 THR Chi-restraints excluded: chain P residue 481 ILE Chi-restraints excluded: chain P residue 489 GLN Chi-restraints excluded: chain P residue 570 MET Chi-restraints excluded: chain P residue 572 MET Chi-restraints excluded: chain P residue 604 PHE Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 218 ILE Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 306 VAL Chi-restraints excluded: chain Q residue 352 HIS Chi-restraints excluded: chain Q residue 397 ASP Chi-restraints excluded: chain Q residue 439 VAL Chi-restraints excluded: chain Q residue 532 VAL Chi-restraints excluded: chain Q residue 535 ILE Chi-restraints excluded: chain Q residue 556 LEU Chi-restraints excluded: chain Q residue 571 VAL Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain S residue 347 ILE Chi-restraints excluded: chain S residue 352 VAL Chi-restraints excluded: chain S residue 371 ASP Chi-restraints excluded: chain S residue 378 VAL Chi-restraints excluded: chain S residue 418 VAL Chi-restraints excluded: chain S residue 441 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 548 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 324 optimal weight: 10.0000 chunk 415 optimal weight: 1.9990 chunk 321 optimal weight: 4.9990 chunk 478 optimal weight: 9.9990 chunk 317 optimal weight: 2.9990 chunk 566 optimal weight: 1.9990 chunk 354 optimal weight: 7.9990 chunk 345 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 380 GLN ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 261 GLN H 566 GLN ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 ASN ** J 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 404 ASN ** P 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 47284 Z= 0.435 Angle : 0.834 11.667 64288 Z= 0.418 Chirality : 0.050 0.318 7316 Planarity : 0.006 0.061 8328 Dihedral : 9.260 77.354 6824 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 35.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 3.88 % Allowed : 25.49 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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: -3.12 (0.10), residues: 5944 helix: -1.70 (0.11), residues: 2028 sheet: -2.60 (0.15), residues: 1000 loop : -2.07 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP I 491 HIS 0.014 0.002 HIS M 488 PHE 0.032 0.002 PHE P 385 TYR 0.037 0.003 TYR R 112 ARG 0.016 0.001 ARG H 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 937 time to evaluate : 5.768 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 429 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7804 (mtm-85) REVERT: A 513 MET cc_start: 0.7967 (mtp) cc_final: 0.7552 (mtt) REVERT: A 544 ASN cc_start: 0.8485 (t0) cc_final: 0.8237 (t0) REVERT: A 561 LEU cc_start: 0.8759 (mt) cc_final: 0.8159 (mp) REVERT: A 568 LEU cc_start: 0.8750 (mm) cc_final: 0.8433 (mm) REVERT: A 570 MET cc_start: 0.8149 (tmm) cc_final: 0.7894 (tpp) REVERT: A 602 LEU cc_start: 0.8794 (mt) cc_final: 0.8357 (mt) REVERT: A 623 GLU cc_start: 0.8932 (tp30) cc_final: 0.8379 (tm-30) REVERT: B 181 ASP cc_start: 0.7594 (t0) cc_final: 0.7042 (t0) REVERT: B 206 PHE cc_start: 0.4904 (t80) cc_final: 0.4272 (t80) REVERT: B 300 LYS cc_start: 0.8145 (tttt) cc_final: 0.7526 (mmtt) REVERT: B 347 HIS cc_start: 0.7516 (OUTLIER) cc_final: 0.7022 (t70) REVERT: B 381 LYS cc_start: 0.7798 (tptm) cc_final: 0.7532 (tppt) REVERT: B 536 ASP cc_start: 0.8296 (m-30) cc_final: 0.7869 (m-30) REVERT: B 544 ASN cc_start: 0.8467 (m-40) cc_final: 0.8102 (m110) REVERT: B 563 LEU cc_start: 0.9110 (tp) cc_final: 0.8818 (tp) REVERT: B 628 MET cc_start: 0.8437 (tmm) cc_final: 0.8213 (tmm) REVERT: F 123 ARG cc_start: 0.6918 (mpt180) cc_final: 0.6176 (mmm160) REVERT: F 141 GLN cc_start: 0.8387 (pt0) cc_final: 0.8176 (pt0) REVERT: F 172 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8354 (ttmt) REVERT: F 221 LYS cc_start: 0.8825 (tptt) cc_final: 0.8517 (pttp) REVERT: F 222 LYS cc_start: 0.8815 (ptmt) cc_final: 0.8526 (pttt) REVERT: G 376 LYS cc_start: 0.9060 (tmtt) cc_final: 0.8709 (tmtt) REVERT: G 382 TYR cc_start: 0.8871 (m-10) cc_final: 0.8499 (m-80) REVERT: G 400 GLU cc_start: 0.7659 (tm-30) cc_final: 0.6582 (tm-30) REVERT: G 402 GLU cc_start: 0.7541 (tt0) cc_final: 0.7213 (tt0) REVERT: H 124 MET cc_start: 0.8020 (ptp) cc_final: 0.7670 (pmm) REVERT: H 198 ARG cc_start: 0.8486 (mtm110) cc_final: 0.7862 (mtp180) REVERT: H 216 ARG cc_start: 0.8323 (tpp80) cc_final: 0.8011 (tpp80) REVERT: H 333 MET cc_start: 0.6470 (mpp) cc_final: 0.5266 (mpp) REVERT: H 513 MET cc_start: 0.6991 (mtp) cc_final: 0.6406 (mtt) REVERT: H 561 LEU cc_start: 0.8653 (mt) cc_final: 0.8105 (mp) REVERT: H 623 GLU cc_start: 0.8839 (tp30) cc_final: 0.8228 (tm-30) REVERT: I 181 ASP cc_start: 0.7537 (t0) cc_final: 0.7066 (t0) REVERT: I 381 LYS cc_start: 0.7774 (tptm) cc_final: 0.7473 (tppt) REVERT: I 466 TYR cc_start: 0.7694 (t80) cc_final: 0.7228 (t80) REVERT: I 536 ASP cc_start: 0.8226 (m-30) cc_final: 0.7638 (m-30) REVERT: J 172 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8393 (ttmm) REVERT: J 221 LYS cc_start: 0.8853 (tptt) cc_final: 0.8470 (pttp) REVERT: K 400 GLU cc_start: 0.7543 (tm-30) cc_final: 0.6477 (tm-30) REVERT: K 402 GLU cc_start: 0.7486 (tt0) cc_final: 0.7144 (tt0) REVERT: L 213 GLU cc_start: 0.8392 (tp30) cc_final: 0.7883 (mm-30) REVERT: L 216 ARG cc_start: 0.8375 (tpp80) cc_final: 0.7805 (tpp80) REVERT: L 333 MET cc_start: 0.6921 (mpp) cc_final: 0.6233 (mpp) REVERT: L 513 MET cc_start: 0.6758 (mtt) cc_final: 0.6454 (mtt) REVERT: L 623 GLU cc_start: 0.8869 (tp30) cc_final: 0.8281 (tm-30) REVERT: M 181 ASP cc_start: 0.7529 (t0) cc_final: 0.6970 (t0) REVERT: M 206 PHE cc_start: 0.5102 (t80) cc_final: 0.4393 (t80) REVERT: M 300 LYS cc_start: 0.8290 (tttt) cc_final: 0.7718 (mmtt) REVERT: M 381 LYS cc_start: 0.7753 (tptm) cc_final: 0.7466 (tppt) REVERT: M 536 ASP cc_start: 0.8157 (m-30) cc_final: 0.7449 (m-30) REVERT: M 628 MET cc_start: 0.8487 (tmm) cc_final: 0.8234 (tmm) REVERT: N 172 LYS cc_start: 0.8762 (ttpt) cc_final: 0.8408 (ttmt) REVERT: N 221 LYS cc_start: 0.8901 (tptt) cc_final: 0.8519 (pttp) REVERT: O 400 GLU cc_start: 0.7543 (tm-30) cc_final: 0.6480 (tm-30) REVERT: O 402 GLU cc_start: 0.7581 (tt0) cc_final: 0.7327 (tt0) REVERT: P 183 LEU cc_start: 0.9160 (tp) cc_final: 0.8915 (tp) REVERT: P 333 MET cc_start: 0.6777 (mpp) cc_final: 0.5430 (mpp) REVERT: P 489 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8016 (tp40) REVERT: P 561 LEU cc_start: 0.8725 (mt) cc_final: 0.8215 (mp) REVERT: P 604 PHE cc_start: 0.8489 (m-80) cc_final: 0.8279 (t80) REVERT: P 623 GLU cc_start: 0.8838 (tp30) cc_final: 0.8311 (tm-30) REVERT: Q 103 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8825 (mm) REVERT: Q 181 ASP cc_start: 0.7346 (t0) cc_final: 0.6718 (t0) REVERT: Q 206 PHE cc_start: 0.5518 (t80) cc_final: 0.4738 (t80) REVERT: Q 216 ARG cc_start: 0.8128 (ttm-80) cc_final: 0.7916 (ttm-80) REVERT: Q 300 LYS cc_start: 0.8229 (tttt) cc_final: 0.7552 (mmtm) REVERT: Q 381 LYS cc_start: 0.7787 (tptm) cc_final: 0.7517 (tppt) REVERT: Q 536 ASP cc_start: 0.8172 (m-30) cc_final: 0.7702 (m-30) REVERT: Q 554 GLU cc_start: 0.7381 (mp0) cc_final: 0.5972 (mm-30) REVERT: Q 563 LEU cc_start: 0.9045 (tp) cc_final: 0.8796 (tp) REVERT: R 112 TYR cc_start: 0.6906 (m-10) cc_final: 0.6538 (m-10) REVERT: R 141 GLN cc_start: 0.8424 (pt0) cc_final: 0.8065 (pt0) REVERT: R 172 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8347 (ttmt) REVERT: R 221 LYS cc_start: 0.8904 (tptt) cc_final: 0.8478 (pttp) REVERT: S 382 TYR cc_start: 0.8819 (m-10) cc_final: 0.8615 (m-80) REVERT: S 400 GLU cc_start: 0.7600 (tm-30) cc_final: 0.6522 (tm-30) REVERT: S 402 GLU cc_start: 0.7602 (tt0) cc_final: 0.7291 (tt0) REVERT: S 441 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7999 (pt) outliers start: 191 outliers final: 150 residues processed: 1060 average time/residue: 0.5767 time to fit residues: 1016.3989 Evaluate side-chains 1036 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 882 time to evaluate : 5.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 487 GLN Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 442 THR Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 457 THR Chi-restraints excluded: chain H residue 554 GLU Chi-restraints excluded: chain H residue 603 LEU Chi-restraints excluded: chain H residue 639 VAL Chi-restraints excluded: chain H residue 641 CYS Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 397 ASP Chi-restraints excluded: chain I residue 439 VAL Chi-restraints excluded: chain I residue 532 VAL Chi-restraints excluded: chain I residue 535 ILE Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain I residue 620 ASP Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain K residue 371 ASP Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 418 VAL Chi-restraints excluded: chain K residue 441 LEU Chi-restraints excluded: chain K residue 442 THR Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 209 THR Chi-restraints excluded: chain L residue 218 ILE Chi-restraints excluded: chain L residue 292 ILE Chi-restraints excluded: chain L residue 457 THR Chi-restraints excluded: chain L residue 641 CYS Chi-restraints excluded: chain L residue 651 ILE Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 218 ILE Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain M residue 359 TYR Chi-restraints excluded: chain M residue 439 VAL Chi-restraints excluded: chain M residue 507 SER Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 532 VAL Chi-restraints excluded: chain M residue 535 ILE Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 556 LEU Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 113 ASN Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 165 GLU Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain O residue 347 ILE Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 360 ILE Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain O residue 378 VAL Chi-restraints excluded: chain O residue 420 ASP Chi-restraints excluded: chain O residue 441 LEU Chi-restraints excluded: chain O residue 442 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 218 ILE Chi-restraints excluded: chain P residue 231 ILE Chi-restraints excluded: chain P residue 443 GLU Chi-restraints excluded: chain P residue 457 THR Chi-restraints excluded: chain P residue 481 ILE Chi-restraints excluded: chain P residue 489 GLN Chi-restraints excluded: chain P residue 572 MET Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 218 ILE Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 306 VAL Chi-restraints excluded: chain Q residue 359 TYR Chi-restraints excluded: chain Q residue 397 ASP Chi-restraints excluded: chain Q residue 439 VAL Chi-restraints excluded: chain Q residue 532 VAL Chi-restraints excluded: chain Q residue 535 ILE Chi-restraints excluded: chain Q residue 556 LEU Chi-restraints excluded: chain Q residue 571 VAL Chi-restraints excluded: chain Q residue 637 LEU Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 136 GLU Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain S residue 329 ILE Chi-restraints excluded: chain S residue 347 ILE Chi-restraints excluded: chain S residue 352 VAL Chi-restraints excluded: chain S residue 360 ILE Chi-restraints excluded: chain S residue 371 ASP Chi-restraints excluded: chain S residue 378 VAL Chi-restraints excluded: chain S residue 418 VAL Chi-restraints excluded: chain S residue 441 LEU Chi-restraints excluded: chain S residue 442 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 350 optimal weight: 5.9990 chunk 226 optimal weight: 0.9990 chunk 338 optimal weight: 0.4980 chunk 170 optimal weight: 1.9990 chunk 111 optimal weight: 0.0070 chunk 109 optimal weight: 0.4980 chunk 360 optimal weight: 0.8980 chunk 386 optimal weight: 3.9990 chunk 280 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 445 optimal weight: 0.5980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN F 122 ASN F 141 GLN ** G 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 261 GLN H 527 ASN ** H 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 269 GLN M 352 HIS ** M 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 494 GLN ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 141 GLN ** S 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 391 HIS ** S 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 47284 Z= 0.220 Angle : 0.752 12.584 64288 Z= 0.367 Chirality : 0.048 0.264 7316 Planarity : 0.005 0.059 8328 Dihedral : 8.990 79.513 6824 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 29.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.09 % Allowed : 27.05 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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: -2.95 (0.10), residues: 5944 helix: -1.48 (0.11), residues: 2020 sheet: -2.56 (0.15), residues: 1028 loop : -1.99 (0.12), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP I 491 HIS 0.013 0.001 HIS M 488 PHE 0.024 0.002 PHE N 107 TYR 0.030 0.002 TYR Q 466 ARG 0.013 0.001 ARG H 198 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1035 time to evaluate : 5.171 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: symmetry clash revert: symmetry clash REVERT: A 240 PHE cc_start: 0.7990 (t80) cc_final: 0.7653 (t80) REVERT: A 294 ARG cc_start: 0.8418 (ptm-80) cc_final: 0.8037 (ptt180) REVERT: A 305 TYR cc_start: 0.7967 (t80) cc_final: 0.7455 (t80) REVERT: A 400 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7329 (tm-30) REVERT: A 504 TRP cc_start: 0.8071 (t-100) cc_final: 0.7654 (t-100) REVERT: A 561 LEU cc_start: 0.8781 (mt) cc_final: 0.8197 (mp) REVERT: A 568 LEU cc_start: 0.8607 (mm) cc_final: 0.8301 (mm) REVERT: A 602 LEU cc_start: 0.8592 (mt) cc_final: 0.7267 (tt) REVERT: A 623 GLU cc_start: 0.8769 (tp30) cc_final: 0.8250 (tm-30) REVERT: B 181 ASP cc_start: 0.7200 (t0) cc_final: 0.6663 (t0) REVERT: B 216 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7109 (ttm-80) REVERT: B 300 LYS cc_start: 0.7855 (tttt) cc_final: 0.7555 (mmtt) REVERT: B 347 HIS cc_start: 0.7428 (OUTLIER) cc_final: 0.6944 (t70) REVERT: B 381 LYS cc_start: 0.7706 (tptm) cc_final: 0.7433 (tppt) REVERT: B 513 MET cc_start: 0.8357 (mtp) cc_final: 0.7718 (ptp) REVERT: B 536 ASP cc_start: 0.7985 (m-30) cc_final: 0.7308 (m-30) REVERT: B 544 ASN cc_start: 0.8367 (m-40) cc_final: 0.8035 (m110) REVERT: B 561 LEU cc_start: 0.8861 (tt) cc_final: 0.8576 (tp) REVERT: B 563 LEU cc_start: 0.9052 (tp) cc_final: 0.8719 (tp) REVERT: F 113 ASN cc_start: 0.7631 (t0) cc_final: 0.7402 (t0) REVERT: F 123 ARG cc_start: 0.6807 (mpt180) cc_final: 0.6273 (mmm160) REVERT: F 172 LYS cc_start: 0.8750 (ttpt) cc_final: 0.8254 (ttmt) REVERT: F 221 LYS cc_start: 0.8645 (tptt) cc_final: 0.8370 (pttp) REVERT: G 376 LYS cc_start: 0.8954 (tmtt) cc_final: 0.8677 (tmtt) REVERT: G 382 TYR cc_start: 0.8652 (m-10) cc_final: 0.8295 (m-80) REVERT: G 400 GLU cc_start: 0.7622 (tm-30) cc_final: 0.6504 (tm-30) REVERT: G 402 GLU cc_start: 0.7816 (tt0) cc_final: 0.7502 (tt0) REVERT: G 441 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7843 (pt) REVERT: G 445 LEU cc_start: 0.8515 (tt) cc_final: 0.8095 (tp) REVERT: H 198 ARG cc_start: 0.8197 (mtm110) cc_final: 0.7488 (mtp180) REVERT: H 216 ARG cc_start: 0.8285 (tpp80) cc_final: 0.7984 (tpp80) REVERT: H 237 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6914 (mt-10) REVERT: H 272 ARG cc_start: 0.8046 (tpp80) cc_final: 0.7728 (tmm-80) REVERT: H 305 TYR cc_start: 0.7975 (t80) cc_final: 0.7501 (t80) REVERT: H 333 MET cc_start: 0.6190 (mpp) cc_final: 0.5358 (mpp) REVERT: H 513 MET cc_start: 0.6368 (mtp) cc_final: 0.6053 (mtt) REVERT: H 559 LYS cc_start: 0.7473 (mmtm) cc_final: 0.7024 (mmtm) REVERT: H 623 GLU cc_start: 0.8751 (tp30) cc_final: 0.8248 (tm-30) REVERT: H 628 MET cc_start: 0.6865 (tpt) cc_final: 0.6649 (tpp) REVERT: I 103 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8889 (mm) REVERT: I 181 ASP cc_start: 0.7178 (t0) cc_final: 0.6786 (t0) REVERT: I 381 LYS cc_start: 0.7650 (tptm) cc_final: 0.7330 (tppt) REVERT: I 466 TYR cc_start: 0.7608 (t80) cc_final: 0.6982 (t80) REVERT: I 536 ASP cc_start: 0.8176 (m-30) cc_final: 0.7615 (m-30) REVERT: I 547 GLU cc_start: 0.7830 (mm-30) cc_final: 0.6973 (mm-30) REVERT: J 172 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8273 (ttmt) REVERT: J 205 GLU cc_start: 0.7393 (tt0) cc_final: 0.6584 (tm-30) REVERT: J 221 LYS cc_start: 0.8771 (tptt) cc_final: 0.8358 (pttp) REVERT: K 400 GLU cc_start: 0.7591 (tm-30) cc_final: 0.6416 (tm-30) REVERT: K 402 GLU cc_start: 0.7657 (tt0) cc_final: 0.7286 (tt0) REVERT: K 445 LEU cc_start: 0.8570 (tt) cc_final: 0.8110 (tp) REVERT: L 333 MET cc_start: 0.6463 (mpp) cc_final: 0.5993 (mpp) REVERT: L 351 MET cc_start: 0.7577 (ttp) cc_final: 0.7237 (ttp) REVERT: L 504 TRP cc_start: 0.7897 (t-100) cc_final: 0.7642 (t-100) REVERT: L 513 MET cc_start: 0.6636 (mtt) cc_final: 0.6314 (mtt) REVERT: L 623 GLU cc_start: 0.8792 (tp30) cc_final: 0.8250 (tm-30) REVERT: L 629 LEU cc_start: 0.8391 (pt) cc_final: 0.7868 (mm) REVERT: M 152 GLU cc_start: 0.6669 (mt-10) cc_final: 0.4448 (mt-10) REVERT: M 181 ASP cc_start: 0.7181 (t0) cc_final: 0.6877 (t70) REVERT: M 206 PHE cc_start: 0.4725 (t80) cc_final: 0.4192 (t80) REVERT: M 216 ARG cc_start: 0.7945 (ttm110) cc_final: 0.7379 (ttm-80) REVERT: M 347 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.6821 (t70) REVERT: M 381 LYS cc_start: 0.7674 (tptm) cc_final: 0.7288 (mmmt) REVERT: M 536 ASP cc_start: 0.7980 (m-30) cc_final: 0.7331 (m-30) REVERT: M 561 LEU cc_start: 0.8890 (tt) cc_final: 0.8602 (tp) REVERT: N 112 TYR cc_start: 0.6619 (m-10) cc_final: 0.6417 (m-10) REVERT: N 172 LYS cc_start: 0.8669 (ttpt) cc_final: 0.8300 (ttmt) REVERT: N 182 GLU cc_start: 0.7188 (tp30) cc_final: 0.6735 (tp30) REVERT: N 221 LYS cc_start: 0.8816 (tptt) cc_final: 0.8407 (pttp) REVERT: O 333 LEU cc_start: 0.9087 (tt) cc_final: 0.8880 (tt) REVERT: O 379 GLN cc_start: 0.8457 (pm20) cc_final: 0.7823 (pm20) REVERT: O 400 GLU cc_start: 0.7507 (tm-30) cc_final: 0.6350 (tm-30) REVERT: O 402 GLU cc_start: 0.7768 (tt0) cc_final: 0.7545 (tt0) REVERT: O 441 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7915 (pt) REVERT: O 445 LEU cc_start: 0.8523 (tt) cc_final: 0.8081 (tp) REVERT: P 144 GLU cc_start: 0.8644 (mp0) cc_final: 0.8320 (mp0) REVERT: P 489 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7761 (tp40) REVERT: P 504 TRP cc_start: 0.7943 (t-100) cc_final: 0.7363 (t-100) REVERT: P 505 LEU cc_start: 0.7980 (mm) cc_final: 0.7643 (mm) REVERT: P 561 LEU cc_start: 0.8664 (mt) cc_final: 0.8145 (mp) REVERT: P 623 GLU cc_start: 0.8786 (tp30) cc_final: 0.8321 (tm-30) REVERT: Q 103 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8878 (mm) REVERT: Q 181 ASP cc_start: 0.7025 (t0) cc_final: 0.6607 (t0) REVERT: Q 216 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7040 (ttm-80) REVERT: Q 381 LYS cc_start: 0.7666 (tptm) cc_final: 0.7342 (tppt) REVERT: Q 403 LYS cc_start: 0.8065 (tppt) cc_final: 0.7367 (tppt) REVERT: Q 536 ASP cc_start: 0.7844 (m-30) cc_final: 0.7211 (m-30) REVERT: Q 554 GLU cc_start: 0.7050 (mp0) cc_final: 0.5763 (mm-30) REVERT: Q 644 GLN cc_start: 0.7758 (pm20) cc_final: 0.7419 (pm20) REVERT: R 141 GLN cc_start: 0.8258 (pt0) cc_final: 0.7793 (pt0) REVERT: R 172 LYS cc_start: 0.8721 (ttpt) cc_final: 0.8277 (ttmt) REVERT: R 205 GLU cc_start: 0.7342 (tt0) cc_final: 0.6596 (tm-30) REVERT: R 221 LYS cc_start: 0.8788 (tptt) cc_final: 0.8375 (pttp) REVERT: S 382 TYR cc_start: 0.8693 (m-10) cc_final: 0.8422 (m-80) REVERT: S 400 GLU cc_start: 0.7633 (tm-30) cc_final: 0.6385 (tm-30) REVERT: S 441 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8069 (pt) REVERT: S 445 LEU cc_start: 0.8544 (tt) cc_final: 0.7950 (tp) outliers start: 152 outliers final: 116 residues processed: 1135 average time/residue: 0.5928 time to fit residues: 1113.0310 Evaluate side-chains 1074 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 950 time to evaluate : 5.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 367 ILE Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 457 THR Chi-restraints excluded: chain H residue 641 CYS Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 348 MET Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 439 VAL Chi-restraints excluded: chain I residue 532 VAL Chi-restraints excluded: chain I residue 535 ILE Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain I residue 620 ASP Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain K residue 371 ASP Chi-restraints excluded: chain K residue 376 LYS Chi-restraints excluded: chain K residue 418 VAL Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 218 ILE Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 292 ILE Chi-restraints excluded: chain L residue 457 THR Chi-restraints excluded: chain L residue 641 CYS Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 218 ILE Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 347 HIS Chi-restraints excluded: chain M residue 359 TYR Chi-restraints excluded: chain M residue 368 LEU Chi-restraints excluded: chain M residue 439 VAL Chi-restraints excluded: chain M residue 532 VAL Chi-restraints excluded: chain M residue 535 ILE Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 556 LEU Chi-restraints excluded: chain M residue 565 ASN Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 165 GLU Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 347 ILE Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain O residue 378 VAL Chi-restraints excluded: chain O residue 441 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 231 ILE Chi-restraints excluded: chain P residue 457 THR Chi-restraints excluded: chain P residue 489 GLN Chi-restraints excluded: chain P residue 572 MET Chi-restraints excluded: chain P residue 650 MET Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 198 ARG Chi-restraints excluded: chain Q residue 218 ILE Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 306 VAL Chi-restraints excluded: chain Q residue 439 VAL Chi-restraints excluded: chain Q residue 532 VAL Chi-restraints excluded: chain Q residue 535 ILE Chi-restraints excluded: chain Q residue 556 LEU Chi-restraints excluded: chain Q residue 637 LEU Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain S residue 329 ILE Chi-restraints excluded: chain S residue 352 VAL Chi-restraints excluded: chain S residue 371 ASP Chi-restraints excluded: chain S residue 418 VAL Chi-restraints excluded: chain S residue 441 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 515 optimal weight: 0.4980 chunk 542 optimal weight: 0.6980 chunk 495 optimal weight: 5.9990 chunk 528 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 414 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 477 optimal weight: 0.0020 chunk 499 optimal weight: 9.9990 chunk 526 optimal weight: 10.0000 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 261 GLN H 527 ASN ** H 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 269 GLN L 489 GLN ** M 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 47284 Z= 0.283 Angle : 0.775 12.911 64288 Z= 0.380 Chirality : 0.048 0.268 7316 Planarity : 0.005 0.062 8328 Dihedral : 8.937 78.989 6824 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 32.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.60 % Favored : 91.39 % Rotamer: Outliers : 2.88 % Allowed : 27.48 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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: -2.93 (0.10), residues: 5944 helix: -1.47 (0.11), residues: 2040 sheet: -2.50 (0.15), residues: 1028 loop : -2.00 (0.11), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP M 491 HIS 0.010 0.001 HIS I 488 PHE 0.027 0.002 PHE H 385 TYR 0.032 0.002 TYR R 112 ARG 0.012 0.001 ARG H 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 975 time to evaluate : 5.261 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 280 MET cc_start: 0.8817 (mmm) cc_final: 0.8536 (mmm) REVERT: A 400 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7362 (tm-30) REVERT: A 504 TRP cc_start: 0.8172 (t-100) cc_final: 0.7675 (t-100) REVERT: A 561 LEU cc_start: 0.8763 (mt) cc_final: 0.8197 (mp) REVERT: A 623 GLU cc_start: 0.8793 (tp30) cc_final: 0.8308 (tm-30) REVERT: B 181 ASP cc_start: 0.7328 (t0) cc_final: 0.6744 (t0) REVERT: B 216 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.6838 (ttm-80) REVERT: B 300 LYS cc_start: 0.7887 (tttt) cc_final: 0.7505 (mmmt) REVERT: B 381 LYS cc_start: 0.7732 (tptm) cc_final: 0.7449 (tppt) REVERT: B 536 ASP cc_start: 0.8047 (m-30) cc_final: 0.7355 (m-30) REVERT: B 544 ASN cc_start: 0.8419 (m-40) cc_final: 0.8097 (m110) REVERT: F 123 ARG cc_start: 0.6874 (mpt180) cc_final: 0.6394 (mmm160) REVERT: F 141 GLN cc_start: 0.7982 (pt0) cc_final: 0.7625 (pt0) REVERT: F 172 LYS cc_start: 0.8784 (ttpt) cc_final: 0.8298 (ttmt) REVERT: F 221 LYS cc_start: 0.8640 (tptt) cc_final: 0.8396 (pttp) REVERT: G 376 LYS cc_start: 0.9042 (tmtt) cc_final: 0.8774 (tmtt) REVERT: G 382 TYR cc_start: 0.8663 (m-10) cc_final: 0.8327 (m-80) REVERT: G 400 GLU cc_start: 0.7689 (tm-30) cc_final: 0.6476 (tm-30) REVERT: G 402 GLU cc_start: 0.7660 (tt0) cc_final: 0.7325 (tt0) REVERT: G 441 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7862 (pt) REVERT: G 445 LEU cc_start: 0.8582 (tt) cc_final: 0.8165 (tp) REVERT: H 198 ARG cc_start: 0.8245 (mtm110) cc_final: 0.7533 (mtp180) REVERT: H 216 ARG cc_start: 0.8274 (tpp80) cc_final: 0.8035 (tpp80) REVERT: H 272 ARG cc_start: 0.8057 (tpp80) cc_final: 0.7830 (tmm-80) REVERT: H 333 MET cc_start: 0.6091 (mpp) cc_final: 0.5413 (mpp) REVERT: H 513 MET cc_start: 0.6546 (mtp) cc_final: 0.6127 (mtt) REVERT: H 536 ASP cc_start: 0.7228 (m-30) cc_final: 0.7007 (m-30) REVERT: H 623 GLU cc_start: 0.8761 (tp30) cc_final: 0.8253 (tm-30) REVERT: I 181 ASP cc_start: 0.7375 (t0) cc_final: 0.6943 (t0) REVERT: I 300 LYS cc_start: 0.7924 (tttt) cc_final: 0.7495 (mmmt) REVERT: I 381 LYS cc_start: 0.7679 (tptm) cc_final: 0.7363 (tppt) REVERT: I 466 TYR cc_start: 0.7576 (t80) cc_final: 0.6973 (t80) REVERT: I 536 ASP cc_start: 0.8043 (m-30) cc_final: 0.7469 (m-30) REVERT: J 140 GLN cc_start: 0.8808 (tp40) cc_final: 0.8561 (tp40) REVERT: J 172 LYS cc_start: 0.8750 (ttpt) cc_final: 0.8330 (ttmm) REVERT: J 184 MET cc_start: 0.7434 (mtt) cc_final: 0.7087 (mtt) REVERT: J 221 LYS cc_start: 0.8798 (tptt) cc_final: 0.8395 (pttp) REVERT: K 400 GLU cc_start: 0.7607 (tm-30) cc_final: 0.6389 (tm-30) REVERT: K 402 GLU cc_start: 0.7550 (tt0) cc_final: 0.7095 (tt0) REVERT: K 445 LEU cc_start: 0.8648 (tt) cc_final: 0.8238 (tp) REVERT: L 216 ARG cc_start: 0.8398 (tpp80) cc_final: 0.8179 (tpp80) REVERT: L 333 MET cc_start: 0.6736 (mpp) cc_final: 0.6388 (mpp) REVERT: L 351 MET cc_start: 0.7571 (ttp) cc_final: 0.7124 (ttp) REVERT: L 504 TRP cc_start: 0.8034 (t-100) cc_final: 0.7774 (t-100) REVERT: L 513 MET cc_start: 0.6623 (mtt) cc_final: 0.6253 (mtt) REVERT: L 623 GLU cc_start: 0.8806 (tp30) cc_final: 0.8260 (tm-30) REVERT: M 152 GLU cc_start: 0.6679 (mt-10) cc_final: 0.5111 (mt-10) REVERT: M 181 ASP cc_start: 0.7352 (t0) cc_final: 0.6885 (t0) REVERT: M 206 PHE cc_start: 0.4554 (t80) cc_final: 0.3873 (t80) REVERT: M 381 LYS cc_start: 0.7704 (tptm) cc_final: 0.7357 (mmmt) REVERT: M 536 ASP cc_start: 0.7943 (m-30) cc_final: 0.7314 (m-30) REVERT: M 629 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7529 (tp) REVERT: N 112 TYR cc_start: 0.6591 (m-10) cc_final: 0.5871 (m-10) REVERT: N 172 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8391 (ttmt) REVERT: N 182 GLU cc_start: 0.7407 (tp30) cc_final: 0.6843 (tt0) REVERT: N 221 LYS cc_start: 0.8793 (tptt) cc_final: 0.8392 (pttp) REVERT: O 400 GLU cc_start: 0.7575 (tm-30) cc_final: 0.6314 (tm-30) REVERT: O 402 GLU cc_start: 0.7803 (tt0) cc_final: 0.7512 (tt0) REVERT: O 441 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7903 (pt) REVERT: O 445 LEU cc_start: 0.8620 (tt) cc_final: 0.8201 (tp) REVERT: P 144 GLU cc_start: 0.8677 (mp0) cc_final: 0.8245 (mp0) REVERT: P 183 LEU cc_start: 0.9086 (tp) cc_final: 0.8810 (tp) REVERT: P 216 ARG cc_start: 0.8340 (tpp80) cc_final: 0.8110 (tpp80) REVERT: P 400 GLU cc_start: 0.7447 (tm-30) cc_final: 0.6996 (tm-30) REVERT: P 489 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7827 (tp40) REVERT: P 504 TRP cc_start: 0.8142 (t-100) cc_final: 0.7407 (t-100) REVERT: P 505 LEU cc_start: 0.8101 (mm) cc_final: 0.7732 (mm) REVERT: P 561 LEU cc_start: 0.8653 (mt) cc_final: 0.8135 (mp) REVERT: P 623 GLU cc_start: 0.8774 (tp30) cc_final: 0.8305 (tm-30) REVERT: Q 103 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8824 (mm) REVERT: Q 181 ASP cc_start: 0.7117 (t0) cc_final: 0.6671 (t0) REVERT: Q 216 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7113 (ttm-80) REVERT: Q 381 LYS cc_start: 0.7684 (tptm) cc_final: 0.7368 (tppt) REVERT: Q 403 LYS cc_start: 0.8096 (tppt) cc_final: 0.7654 (tppt) REVERT: Q 536 ASP cc_start: 0.7935 (m-30) cc_final: 0.7249 (m-30) REVERT: Q 554 GLU cc_start: 0.7085 (mp0) cc_final: 0.5903 (mm-30) REVERT: R 112 TYR cc_start: 0.6583 (m-10) cc_final: 0.6002 (m-10) REVERT: R 113 ASN cc_start: 0.8002 (t0) cc_final: 0.7766 (t0) REVERT: R 141 GLN cc_start: 0.8201 (pt0) cc_final: 0.7777 (pt0) REVERT: R 172 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8374 (ttmt) REVERT: R 182 GLU cc_start: 0.7451 (tt0) cc_final: 0.7202 (tp30) REVERT: R 221 LYS cc_start: 0.8790 (tptt) cc_final: 0.8391 (pttp) REVERT: S 382 TYR cc_start: 0.8693 (m-10) cc_final: 0.8422 (m-80) REVERT: S 400 GLU cc_start: 0.7650 (tm-30) cc_final: 0.6378 (tm-30) REVERT: S 402 GLU cc_start: 0.7956 (tt0) cc_final: 0.7681 (tt0) REVERT: S 416 ARG cc_start: 0.7552 (tpt90) cc_final: 0.7256 (tpm170) REVERT: S 441 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8064 (pt) REVERT: S 445 LEU cc_start: 0.8641 (tt) cc_final: 0.8242 (tp) outliers start: 142 outliers final: 120 residues processed: 1071 average time/residue: 0.5844 time to fit residues: 1037.9167 Evaluate side-chains 1057 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 931 time to evaluate : 5.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 367 ILE Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 457 THR Chi-restraints excluded: chain H residue 641 CYS Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 439 VAL Chi-restraints excluded: chain I residue 513 MET Chi-restraints excluded: chain I residue 532 VAL Chi-restraints excluded: chain I residue 535 ILE Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 113 ASN Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain K residue 371 ASP Chi-restraints excluded: chain K residue 376 LYS Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 418 VAL Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 218 ILE Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 292 ILE Chi-restraints excluded: chain L residue 457 THR Chi-restraints excluded: chain L residue 641 CYS Chi-restraints excluded: chain L residue 651 ILE Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 218 ILE Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 359 TYR Chi-restraints excluded: chain M residue 439 VAL Chi-restraints excluded: chain M residue 532 VAL Chi-restraints excluded: chain M residue 535 ILE Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 556 LEU Chi-restraints excluded: chain M residue 629 LEU Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 PHE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 165 GLU Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 360 ILE Chi-restraints excluded: chain O residue 367 ILE Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain O residue 378 VAL Chi-restraints excluded: chain O residue 441 LEU Chi-restraints excluded: chain O residue 442 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 231 ILE Chi-restraints excluded: chain P residue 271 MET Chi-restraints excluded: chain P residue 457 THR Chi-restraints excluded: chain P residue 489 GLN Chi-restraints excluded: chain P residue 572 MET Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 198 ARG Chi-restraints excluded: chain Q residue 218 ILE Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 306 VAL Chi-restraints excluded: chain Q residue 352 HIS Chi-restraints excluded: chain Q residue 439 VAL Chi-restraints excluded: chain Q residue 532 VAL Chi-restraints excluded: chain Q residue 535 ILE Chi-restraints excluded: chain Q residue 556 LEU Chi-restraints excluded: chain Q residue 571 VAL Chi-restraints excluded: chain Q residue 637 LEU Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain S residue 329 ILE Chi-restraints excluded: chain S residue 352 VAL Chi-restraints excluded: chain S residue 371 ASP Chi-restraints excluded: chain S residue 378 VAL Chi-restraints excluded: chain S residue 418 VAL Chi-restraints excluded: chain S residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 346 optimal weight: 5.9990 chunk 558 optimal weight: 0.0270 chunk 340 optimal weight: 0.0170 chunk 264 optimal weight: 3.9990 chunk 388 optimal weight: 0.6980 chunk 585 optimal weight: 2.9990 chunk 539 optimal weight: 0.9980 chunk 466 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 360 optimal weight: 0.0010 chunk 286 optimal weight: 0.7980 overall best weight: 0.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN ** G 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 489 GLN H 527 ASN ** H 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 127 HIS L 269 GLN ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 352 HIS ** M 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 127 HIS ** P 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 527 ASN ** Q 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 391 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 47284 Z= 0.216 Angle : 0.772 13.978 64288 Z= 0.374 Chirality : 0.048 0.262 7316 Planarity : 0.005 0.062 8328 Dihedral : 8.747 80.583 6824 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 28.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.36 % Allowed : 28.11 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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: -2.86 (0.10), residues: 5944 helix: -1.35 (0.11), residues: 2040 sheet: -2.36 (0.15), residues: 1028 loop : -2.06 (0.11), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP B 504 HIS 0.011 0.001 HIS B 488 PHE 0.035 0.002 PHE P 541 TYR 0.033 0.002 TYR B 466 ARG 0.016 0.001 ARG I 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11888 Ramachandran restraints generated. 5944 Oldfield, 0 Emsley, 5944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1049 time to evaluate : 5.112 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: A 124 MET cc_start: 0.7869 (pmm) cc_final: 0.7445 (pmm) REVERT: A 280 MET cc_start: 0.8809 (mmm) cc_final: 0.8508 (mmm) REVERT: A 305 TYR cc_start: 0.8016 (t80) cc_final: 0.7557 (t80) REVERT: A 310 CYS cc_start: 0.8995 (m) cc_final: 0.7773 (p) REVERT: A 400 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7270 (tm-30) REVERT: A 504 TRP cc_start: 0.7696 (t-100) cc_final: 0.7347 (t-100) REVERT: A 543 MET cc_start: 0.6952 (mtp) cc_final: 0.6529 (mtp) REVERT: A 561 LEU cc_start: 0.8659 (mt) cc_final: 0.8116 (mp) REVERT: A 623 GLU cc_start: 0.8762 (tp30) cc_final: 0.8298 (tm-30) REVERT: B 181 ASP cc_start: 0.7061 (t0) cc_final: 0.6528 (t0) REVERT: B 216 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7286 (ttm110) REVERT: B 300 LYS cc_start: 0.7953 (tttt) cc_final: 0.7638 (mmmt) REVERT: B 381 LYS cc_start: 0.7639 (tptm) cc_final: 0.7271 (tppt) REVERT: B 513 MET cc_start: 0.8086 (mtp) cc_final: 0.7853 (ptp) REVERT: B 536 ASP cc_start: 0.8121 (m-30) cc_final: 0.7522 (m-30) REVERT: B 544 ASN cc_start: 0.8349 (m-40) cc_final: 0.8026 (m110) REVERT: B 561 LEU cc_start: 0.8830 (tt) cc_final: 0.8540 (tp) REVERT: B 566 GLN cc_start: 0.7548 (mm110) cc_final: 0.7231 (mm110) REVERT: F 123 ARG cc_start: 0.6953 (mpt180) cc_final: 0.6334 (mmm160) REVERT: F 141 GLN cc_start: 0.7782 (pt0) cc_final: 0.7486 (pt0) REVERT: F 172 LYS cc_start: 0.8748 (ttpt) cc_final: 0.8272 (ttmt) REVERT: F 184 MET cc_start: 0.7400 (mtt) cc_final: 0.6916 (mtt) REVERT: F 221 LYS cc_start: 0.8647 (tptt) cc_final: 0.8374 (pttp) REVERT: G 333 LEU cc_start: 0.8999 (tt) cc_final: 0.8753 (tt) REVERT: G 379 GLN cc_start: 0.8526 (pm20) cc_final: 0.7696 (pm20) REVERT: G 382 TYR cc_start: 0.8566 (m-10) cc_final: 0.8244 (m-80) REVERT: G 400 GLU cc_start: 0.7646 (tm-30) cc_final: 0.6483 (tm-30) REVERT: G 402 GLU cc_start: 0.7901 (tt0) cc_final: 0.7325 (tt0) REVERT: G 441 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7804 (pt) REVERT: G 445 LEU cc_start: 0.8542 (tt) cc_final: 0.8247 (tp) REVERT: G 448 MET cc_start: 0.7955 (mpp) cc_final: 0.7703 (mmp) REVERT: H 198 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7479 (mtp180) REVERT: H 216 ARG cc_start: 0.8178 (tpp80) cc_final: 0.7908 (tpp80) REVERT: H 294 ARG cc_start: 0.8461 (ptm-80) cc_final: 0.7729 (mmm160) REVERT: H 474 LEU cc_start: 0.8210 (mt) cc_final: 0.7960 (mp) REVERT: H 513 MET cc_start: 0.6418 (mtp) cc_final: 0.6091 (mtt) REVERT: H 623 GLU cc_start: 0.8691 (tp30) cc_final: 0.8276 (tm-30) REVERT: I 181 ASP cc_start: 0.7063 (t0) cc_final: 0.6688 (t0) REVERT: I 300 LYS cc_start: 0.7969 (tttt) cc_final: 0.7621 (mmmt) REVERT: I 381 LYS cc_start: 0.7589 (tptm) cc_final: 0.7247 (tppt) REVERT: I 422 MET cc_start: 0.8024 (mmm) cc_final: 0.7686 (tpt) REVERT: I 466 TYR cc_start: 0.7503 (t80) cc_final: 0.6974 (t80) REVERT: I 536 ASP cc_start: 0.7736 (m-30) cc_final: 0.7111 (m-30) REVERT: I 547 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7027 (mm-30) REVERT: I 554 GLU cc_start: 0.7101 (mp0) cc_final: 0.5561 (mm-30) REVERT: I 601 MET cc_start: 0.7091 (mmp) cc_final: 0.6854 (mmp) REVERT: I 628 MET cc_start: 0.7144 (mtt) cc_final: 0.6922 (mtt) REVERT: J 140 GLN cc_start: 0.8801 (tp40) cc_final: 0.8577 (tp40) REVERT: J 184 MET cc_start: 0.7404 (mtt) cc_final: 0.6982 (mtt) REVERT: J 221 LYS cc_start: 0.8705 (tptt) cc_final: 0.8252 (pttp) REVERT: K 400 GLU cc_start: 0.7641 (tm-30) cc_final: 0.6276 (tm-30) REVERT: K 402 GLU cc_start: 0.7707 (tt0) cc_final: 0.7444 (tt0) REVERT: K 445 LEU cc_start: 0.8552 (tt) cc_final: 0.7953 (tp) REVERT: L 124 MET cc_start: 0.7765 (pmm) cc_final: 0.7555 (pmm) REVERT: L 144 GLU cc_start: 0.8665 (mp0) cc_final: 0.8432 (mp0) REVERT: L 489 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7919 (tp40) REVERT: L 504 TRP cc_start: 0.7644 (t-100) cc_final: 0.7342 (t-100) REVERT: L 513 MET cc_start: 0.6555 (mtt) cc_final: 0.6215 (mtt) REVERT: L 623 GLU cc_start: 0.8718 (tp30) cc_final: 0.8262 (tm-30) REVERT: M 181 ASP cc_start: 0.7195 (t0) cc_final: 0.6783 (t0) REVERT: M 206 PHE cc_start: 0.4544 (t80) cc_final: 0.4176 (t80) REVERT: M 381 LYS cc_start: 0.7613 (tptm) cc_final: 0.7219 (mmmt) REVERT: M 536 ASP cc_start: 0.7515 (m-30) cc_final: 0.6718 (m-30) REVERT: M 561 LEU cc_start: 0.8630 (tt) cc_final: 0.8234 (tp) REVERT: N 172 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8549 (ttmt) REVERT: N 182 GLU cc_start: 0.7193 (tp30) cc_final: 0.6614 (tt0) REVERT: N 184 MET cc_start: 0.7314 (mtt) cc_final: 0.6959 (mtt) REVERT: N 221 LYS cc_start: 0.8754 (tptt) cc_final: 0.8305 (pttp) REVERT: O 379 GLN cc_start: 0.8449 (pm20) cc_final: 0.7830 (pm20) REVERT: O 400 GLU cc_start: 0.7564 (tm-30) cc_final: 0.6257 (tm-30) REVERT: O 402 GLU cc_start: 0.7893 (tt0) cc_final: 0.7388 (tt0) REVERT: O 441 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8005 (pt) REVERT: O 445 LEU cc_start: 0.8531 (tt) cc_final: 0.8223 (tp) REVERT: O 448 MET cc_start: 0.8033 (mpp) cc_final: 0.7685 (mmp) REVERT: P 144 GLU cc_start: 0.8489 (mp0) cc_final: 0.8080 (mp0) REVERT: P 183 LEU cc_start: 0.9015 (tp) cc_final: 0.8690 (tp) REVERT: P 216 ARG cc_start: 0.8285 (tpp80) cc_final: 0.8054 (tpp80) REVERT: P 400 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6991 (tm-30) REVERT: P 474 LEU cc_start: 0.8363 (mt) cc_final: 0.7959 (mm) REVERT: P 489 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7642 (tp40) REVERT: P 504 TRP cc_start: 0.7815 (t-100) cc_final: 0.7348 (t-100) REVERT: P 505 LEU cc_start: 0.8030 (mm) cc_final: 0.7670 (mm) REVERT: P 561 LEU cc_start: 0.8552 (mt) cc_final: 0.8026 (mp) REVERT: P 623 GLU cc_start: 0.8760 (tp30) cc_final: 0.8341 (tm-30) REVERT: Q 103 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8843 (mm) REVERT: Q 206 PHE cc_start: 0.4374 (t80) cc_final: 0.3948 (t80) REVERT: Q 216 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.7091 (ttm-80) REVERT: Q 300 LYS cc_start: 0.7815 (tttt) cc_final: 0.7456 (mmmt) REVERT: Q 381 LYS cc_start: 0.7591 (tptm) cc_final: 0.7221 (mmmt) REVERT: Q 536 ASP cc_start: 0.7592 (m-30) cc_final: 0.6886 (m-30) REVERT: Q 554 GLU cc_start: 0.6736 (mp0) cc_final: 0.5645 (mm-30) REVERT: Q 644 GLN cc_start: 0.7740 (pm20) cc_final: 0.7371 (pm20) REVERT: R 112 TYR cc_start: 0.6550 (m-10) cc_final: 0.5994 (m-10) REVERT: R 113 ASN cc_start: 0.7837 (t0) cc_final: 0.7631 (t0) REVERT: R 141 GLN cc_start: 0.8111 (pt0) cc_final: 0.7901 (pt0) REVERT: R 172 LYS cc_start: 0.8713 (ttpt) cc_final: 0.8266 (ttmt) REVERT: R 182 GLU cc_start: 0.7429 (tt0) cc_final: 0.7180 (tp30) REVERT: R 205 GLU cc_start: 0.7209 (tt0) cc_final: 0.6473 (tm-30) REVERT: R 221 LYS cc_start: 0.8711 (tptt) cc_final: 0.8318 (pttp) REVERT: S 382 TYR cc_start: 0.8615 (m-10) cc_final: 0.8330 (m-80) REVERT: S 400 GLU cc_start: 0.7648 (tm-30) cc_final: 0.6395 (tm-30) REVERT: S 402 GLU cc_start: 0.7954 (tt0) cc_final: 0.7671 (tt0) REVERT: S 441 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7979 (pt) REVERT: S 445 LEU cc_start: 0.8574 (tt) cc_final: 0.8178 (tp) outliers start: 116 outliers final: 101 residues processed: 1127 average time/residue: 0.5750 time to fit residues: 1075.7701 Evaluate side-chains 1087 residues out of total 4940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 980 time to evaluate : 5.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 367 ILE Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 457 THR Chi-restraints excluded: chain H residue 641 CYS Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 439 VAL Chi-restraints excluded: chain I residue 513 MET Chi-restraints excluded: chain I residue 532 VAL Chi-restraints excluded: chain I residue 535 ILE Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain K residue 371 ASP Chi-restraints excluded: chain K residue 376 LYS Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 218 ILE Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 457 THR Chi-restraints excluded: chain L residue 489 GLN Chi-restraints excluded: chain L residue 641 CYS Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 359 TYR Chi-restraints excluded: chain M residue 439 VAL Chi-restraints excluded: chain M residue 535 ILE Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 556 LEU Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 PHE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 165 GLU Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 367 ILE Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain O residue 378 VAL Chi-restraints excluded: chain O residue 441 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 231 ILE Chi-restraints excluded: chain P residue 457 THR Chi-restraints excluded: chain P residue 489 GLN Chi-restraints excluded: chain P residue 572 MET Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 218 ILE Chi-restraints excluded: chain Q residue 439 VAL Chi-restraints excluded: chain Q residue 535 ILE Chi-restraints excluded: chain Q residue 571 VAL Chi-restraints excluded: chain Q residue 637 LEU Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 136 GLU Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain S residue 352 VAL Chi-restraints excluded: chain S residue 367 ILE Chi-restraints excluded: chain S residue 371 ASP Chi-restraints excluded: chain S residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 370 optimal weight: 0.0470 chunk 496 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 430 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 467 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 479 optimal weight: 0.0000 chunk 59 optimal weight: 0.0970 chunk 86 optimal weight: 0.0470 overall best weight: 0.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 391 HIS ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 269 GLN ** H 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 527 ASN ** H 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 440 GLN ** M 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 334 ASN ** P 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 527 ASN ** Q 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 391 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.124179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.102555 restraints weight = 244961.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.106983 restraints weight = 119499.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.108970 restraints weight = 66546.251| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 47284 Z= 0.217 Angle : 0.772 13.577 64288 Z= 0.375 Chirality : 0.048 0.249 7316 Planarity : 0.005 0.065 8328 Dihedral : 8.570 84.604 6824 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 28.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.27 % Allowed : 28.98 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.10), residues: 5944 helix: -1.30 (0.11), residues: 2020 sheet: -2.21 (0.15), residues: 1028 loop : -2.04 (0.11), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP Q 491 HIS 0.010 0.001 HIS I 488 PHE 0.034 0.002 PHE P 541 TYR 0.030 0.002 TYR Q 466 ARG 0.012 0.001 ARG H 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15678.90 seconds wall clock time: 279 minutes 4.86 seconds (16744.86 seconds total)