Starting phenix.real_space_refine on Mon Mar 18 23:11:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmu_0920/03_2024/6lmu_0920.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmu_0920/03_2024/6lmu_0920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmu_0920/03_2024/6lmu_0920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmu_0920/03_2024/6lmu_0920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmu_0920/03_2024/6lmu_0920.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmu_0920/03_2024/6lmu_0920.pdb" } resolution = 3.4 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 14553 2.51 5 N 4026 2.21 5 O 3762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 109": "NH1" <-> "NH2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 259": "OD1" <-> "OD2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 259": "OD1" <-> "OD2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 259": "OD1" <-> "OD2" Residue "E GLU 261": "OE1" <-> "OE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 259": "OD1" <-> "OD2" Residue "F GLU 261": "OE1" <-> "OE2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 179": "NH1" <-> "NH2" Residue "G TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 259": "OD1" <-> "OD2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 270": "OE1" <-> "OE2" Residue "H ARG 109": "NH1" <-> "NH2" Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 159": "NH1" <-> "NH2" Residue "H PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 179": "NH1" <-> "NH2" Residue "H TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 259": "OD1" <-> "OD2" Residue "H GLU 261": "OE1" <-> "OE2" Residue "H PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 270": "OE1" <-> "OE2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 159": "NH1" <-> "NH2" Residue "I PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 179": "NH1" <-> "NH2" Residue "I TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 259": "OD1" <-> "OD2" Residue "I GLU 261": "OE1" <-> "OE2" Residue "I PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 270": "OE1" <-> "OE2" Residue "J ARG 109": "NH1" <-> "NH2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 159": "NH1" <-> "NH2" Residue "J PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 179": "NH1" <-> "NH2" Residue "J TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 259": "OD1" <-> "OD2" Residue "J GLU 261": "OE1" <-> "OE2" Residue "J PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 270": "OE1" <-> "OE2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 159": "NH1" <-> "NH2" Residue "K PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 179": "NH1" <-> "NH2" Residue "K TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 259": "OD1" <-> "OD2" Residue "K GLU 261": "OE1" <-> "OE2" Residue "K PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 270": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22429 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2039 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2039 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2039 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "D" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2039 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "E" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2039 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2039 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "G" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2039 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "H" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2039 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "I" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2039 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "J" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2039 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "K" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2039 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Time building chain proxies: 11.98, per 1000 atoms: 0.53 Number of scatterers: 22429 At special positions: 0 Unit cell: (152.513, 153.874, 100.767, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 3762 8.00 N 4026 7.00 C 14553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 130 " distance=2.04 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 130 " distance=2.04 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 130 " distance=2.04 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 130 " distance=2.04 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 130 " distance=2.04 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 130 " distance=2.04 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 130 " distance=2.04 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 130 " distance=2.04 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 162 " distance=2.03 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 130 " distance=2.04 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 130 " distance=2.04 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 130 " distance=2.04 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 162 " distance=2.03 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: 7.93 Conformation dependent library (CDL) restraints added in 4.2 seconds 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5522 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 11 sheets defined 69.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 58 " --> pdb=" O TYR A 54 " (cutoff:3.500A) Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 79 through 88 removed outlier: 4.094A pdb=" N HIS A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS A 92 " --> pdb=" O ARG A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE A 156 " --> pdb=" O HIS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 169 through 207 Processing helix chain 'A' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 58 " --> pdb=" O TYR B 54 " (cutoff:3.500A) Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS B 92 " --> pdb=" O ARG B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 124 removed outlier: 3.580A pdb=" N ARG B 124 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 135 Processing helix chain 'B' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE B 156 " --> pdb=" O HIS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 207 removed outlier: 3.500A pdb=" N ARG B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 251 removed outlier: 3.541A pdb=" N ALA B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU C 58 " --> pdb=" O TYR C 54 " (cutoff:3.500A) Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS C 92 " --> pdb=" O ARG C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG C 124 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE C 156 " --> pdb=" O HIS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 169 through 207 Processing helix chain 'C' and resid 214 through 251 removed outlier: 3.541A pdb=" N ALA C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 232 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 274 through 280 Processing helix chain 'C' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU D 58 " --> pdb=" O TYR D 54 " (cutoff:3.500A) Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 92 removed outlier: 3.639A pdb=" N LYS D 92 " --> pdb=" O ARG D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 92' Processing helix chain 'D' and resid 99 through 113 removed outlier: 3.908A pdb=" N ALA D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 124 removed outlier: 3.580A pdb=" N ARG D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 Processing helix chain 'D' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE D 156 " --> pdb=" O HIS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 169 through 207 removed outlier: 3.500A pdb=" N ARG D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 251 removed outlier: 3.541A pdb=" N ALA D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN D 232 " --> pdb=" O ASP D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 274 through 280 Processing helix chain 'D' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP D 302 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU E 58 " --> pdb=" O TYR E 54 " (cutoff:3.500A) Proline residue: E 64 - end of helix Processing helix chain 'E' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS E 92 " --> pdb=" O ARG E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 92' Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.906A pdb=" N ALA E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 152 through 158 removed outlier: 4.058A pdb=" N ILE E 156 " --> pdb=" O HIS E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 169 through 207 Processing helix chain 'E' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 232 " --> pdb=" O ASP E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 274 through 280 Processing helix chain 'E' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP E 302 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR F 56 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY F 57 " --> pdb=" O ASN F 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU F 58 " --> pdb=" O TYR F 54 " (cutoff:3.500A) Proline residue: F 64 - end of helix Processing helix chain 'F' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS F 92 " --> pdb=" O ARG F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 89 through 92' Processing helix chain 'F' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 135 Processing helix chain 'F' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE F 156 " --> pdb=" O HIS F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 169 through 207 Processing helix chain 'F' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 267 Processing helix chain 'F' and resid 274 through 280 Processing helix chain 'F' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP F 302 " --> pdb=" O ARG F 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR G 56 " --> pdb=" O ARG G 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY G 57 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU G 58 " --> pdb=" O TYR G 54 " (cutoff:3.500A) Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 79 through 88 removed outlier: 4.094A pdb=" N HIS G 88 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS G 92 " --> pdb=" O ARG G 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 89 through 92' Processing helix chain 'G' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA G 113 " --> pdb=" O ARG G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG G 124 " --> pdb=" O ILE G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 135 Processing helix chain 'G' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE G 156 " --> pdb=" O HIS G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 169 through 207 Processing helix chain 'G' and resid 214 through 251 removed outlier: 3.541A pdb=" N ALA G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN G 232 " --> pdb=" O ASP G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 267 Processing helix chain 'G' and resid 274 through 280 Processing helix chain 'G' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP G 302 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR H 56 " --> pdb=" O ARG H 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY H 57 " --> pdb=" O ASN H 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU H 58 " --> pdb=" O TYR H 54 " (cutoff:3.500A) Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS H 88 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 92 removed outlier: 3.639A pdb=" N LYS H 92 " --> pdb=" O ARG H 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 89 through 92' Processing helix chain 'H' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA H 113 " --> pdb=" O ARG H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG H 124 " --> pdb=" O ILE H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 135 Processing helix chain 'H' and resid 152 through 158 removed outlier: 4.058A pdb=" N ILE H 156 " --> pdb=" O HIS H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 169 through 207 Processing helix chain 'H' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 267 Processing helix chain 'H' and resid 274 through 280 Processing helix chain 'H' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP H 302 " --> pdb=" O ARG H 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY I 57 " --> pdb=" O ASN I 53 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU I 58 " --> pdb=" O TYR I 54 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'I' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS I 88 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 92 removed outlier: 3.639A pdb=" N LYS I 92 " --> pdb=" O ARG I 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 89 through 92' Processing helix chain 'I' and resid 99 through 113 removed outlier: 3.908A pdb=" N ALA I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 124 removed outlier: 3.580A pdb=" N ARG I 124 " --> pdb=" O ILE I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 135 Processing helix chain 'I' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE I 156 " --> pdb=" O HIS I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 207 Processing helix chain 'I' and resid 214 through 251 removed outlier: 3.541A pdb=" N ALA I 225 " --> pdb=" O ALA I 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN I 232 " --> pdb=" O ASP I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 267 Processing helix chain 'I' and resid 274 through 280 Processing helix chain 'I' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP I 302 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR J 56 " --> pdb=" O ARG J 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY J 57 " --> pdb=" O ASN J 53 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU J 58 " --> pdb=" O TYR J 54 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'J' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS J 88 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS J 92 " --> pdb=" O ARG J 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 89 through 92' Processing helix chain 'J' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA J 113 " --> pdb=" O ARG J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 135 Processing helix chain 'J' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE J 156 " --> pdb=" O HIS J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 169 through 207 Processing helix chain 'J' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN J 232 " --> pdb=" O ASP J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 267 Processing helix chain 'J' and resid 274 through 280 Processing helix chain 'J' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP J 302 " --> pdb=" O ARG J 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY K 57 " --> pdb=" O ASN K 53 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU K 58 " --> pdb=" O TYR K 54 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS K 88 " --> pdb=" O ALA K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS K 92 " --> pdb=" O ARG K 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 89 through 92' Processing helix chain 'K' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA K 113 " --> pdb=" O ARG K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 124 removed outlier: 3.580A pdb=" N ARG K 124 " --> pdb=" O ILE K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 135 Processing helix chain 'K' and resid 152 through 158 removed outlier: 4.058A pdb=" N ILE K 156 " --> pdb=" O HIS K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 168 No H-bonds generated for 'chain 'K' and resid 166 through 168' Processing helix chain 'K' and resid 169 through 207 Processing helix chain 'K' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA K 225 " --> pdb=" O ALA K 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN K 232 " --> pdb=" O ASP K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 267 Processing helix chain 'K' and resid 274 through 280 Processing helix chain 'K' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP K 302 " --> pdb=" O ARG K 298 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.845A pdb=" N ARG A 288 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 295 " --> pdb=" O ARG A 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG B 288 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 295 " --> pdb=" O ARG B 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG C 288 " --> pdb=" O LEU C 295 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 295 " --> pdb=" O ARG C 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG D 288 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 295 " --> pdb=" O ARG D 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 288 through 289 removed outlier: 3.845A pdb=" N ARG E 288 " --> pdb=" O LEU E 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU E 295 " --> pdb=" O ARG E 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG F 288 " --> pdb=" O LEU F 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 295 " --> pdb=" O ARG F 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 288 through 289 removed outlier: 3.845A pdb=" N ARG G 288 " --> pdb=" O LEU G 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU G 295 " --> pdb=" O ARG G 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 288 through 289 removed outlier: 3.845A pdb=" N ARG H 288 " --> pdb=" O LEU H 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU H 295 " --> pdb=" O ARG H 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'I' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG I 288 " --> pdb=" O LEU I 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU I 295 " --> pdb=" O ARG I 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG J 288 " --> pdb=" O LEU J 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU J 295 " --> pdb=" O ARG J 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG K 288 " --> pdb=" O LEU K 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU K 295 " --> pdb=" O ARG K 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 1307 hydrogen bonds defined for protein. 3855 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: 6.10 Time building geometry restraints manager: 8.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7205 1.34 - 1.46: 5886 1.46 - 1.58: 9888 1.58 - 1.71: 0 1.71 - 1.83: 88 Bond restraints: 23067 Sorted by residual: bond pdb=" CB THR C 234 " pdb=" CG2 THR C 234 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.07e+00 bond pdb=" CB THR F 234 " pdb=" CG2 THR F 234 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.07e+00 bond pdb=" CB THR G 234 " pdb=" CG2 THR G 234 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.07e+00 bond pdb=" CB THR H 234 " pdb=" CG2 THR H 234 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.06e+00 bond pdb=" CB THR E 234 " pdb=" CG2 THR E 234 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.06e+00 ... (remaining 23062 not shown) Histogram of bond angle deviations from ideal: 101.99 - 108.40: 1448 108.40 - 114.81: 12505 114.81 - 121.22: 11949 121.22 - 127.64: 5239 127.64 - 134.05: 385 Bond angle restraints: 31526 Sorted by residual: angle pdb=" C ASN H 290 " pdb=" N GLN H 291 " pdb=" CA GLN H 291 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C ASN I 290 " pdb=" N GLN I 291 " pdb=" CA GLN I 291 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C ASN B 290 " pdb=" N GLN B 291 " pdb=" CA GLN B 291 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C ASN C 290 " pdb=" N GLN C 291 " pdb=" CA GLN C 291 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C ASN J 290 " pdb=" N GLN J 291 " pdb=" CA GLN J 291 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 ... (remaining 31521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 11409 15.13 - 30.26: 1428 30.26 - 45.39: 539 45.39 - 60.52: 132 60.52 - 75.65: 44 Dihedral angle restraints: 13552 sinusoidal: 5027 harmonic: 8525 Sorted by residual: dihedral pdb=" CB CYS J 46 " pdb=" SG CYS J 46 " pdb=" SG CYS J 130 " pdb=" CB CYS J 130 " ideal model delta sinusoidal sigma weight residual 93.00 168.65 -75.65 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" CB CYS I 46 " pdb=" SG CYS I 46 " pdb=" SG CYS I 130 " pdb=" CB CYS I 130 " ideal model delta sinusoidal sigma weight residual 93.00 168.63 -75.63 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" CB CYS D 46 " pdb=" SG CYS D 46 " pdb=" SG CYS D 130 " pdb=" CB CYS D 130 " ideal model delta sinusoidal sigma weight residual 93.00 168.63 -75.63 1 1.00e+01 1.00e-02 7.22e+01 ... (remaining 13549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1661 0.036 - 0.071: 1265 0.071 - 0.107: 325 0.107 - 0.143: 203 0.143 - 0.178: 66 Chirality restraints: 3520 Sorted by residual: chirality pdb=" CB VAL B 284 " pdb=" CA VAL B 284 " pdb=" CG1 VAL B 284 " pdb=" CG2 VAL B 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CB VAL C 284 " pdb=" CA VAL C 284 " pdb=" CG1 VAL C 284 " pdb=" CG2 VAL C 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB VAL I 284 " pdb=" CA VAL I 284 " pdb=" CG1 VAL I 284 " pdb=" CG2 VAL I 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 3517 not shown) Planarity restraints: 4048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 275 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO I 276 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO I 276 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO I 276 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 275 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO B 276 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 275 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO E 276 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 276 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 276 " 0.038 5.00e-02 4.00e+02 ... (remaining 4045 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 7587 2.84 - 3.35: 20366 3.35 - 3.87: 35871 3.87 - 4.38: 39664 4.38 - 4.90: 67774 Nonbonded interactions: 171262 Sorted by model distance: nonbonded pdb=" O SER I 121 " pdb=" OG SER I 121 " model vdw 2.320 2.440 nonbonded pdb=" O SER A 121 " pdb=" OG SER A 121 " model vdw 2.320 2.440 nonbonded pdb=" O SER F 121 " pdb=" OG SER F 121 " model vdw 2.320 2.440 nonbonded pdb=" O SER H 121 " pdb=" OG SER H 121 " model vdw 2.320 2.440 nonbonded pdb=" O SER B 121 " pdb=" OG SER B 121 " model vdw 2.320 2.440 ... (remaining 171257 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 0.020 Extract box with map and model: 2.860 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 55.850 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 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 : 0.010 0.067 23067 Z= 0.666 Angle : 1.157 8.683 31526 Z= 0.647 Chirality : 0.057 0.178 3520 Planarity : 0.007 0.068 4048 Dihedral : 16.070 69.241 7964 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 1.50 % Allowed : 14.50 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.98 (0.11), residues: 2871 helix: -4.07 (0.06), residues: 1749 sheet: None (None), residues: 0 loop : -3.54 (0.16), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 220 HIS 0.008 0.002 HIS D 88 PHE 0.016 0.003 PHE F 253 TYR 0.033 0.004 TYR E 182 ARG 0.006 0.001 ARG K 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 320 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7632 (pp20) cc_final: 0.6947 (pp20) REVERT: A 277 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7522 (mm110) REVERT: B 262 GLU cc_start: 0.7462 (pp20) cc_final: 0.6827 (pp20) REVERT: D 293 LEU cc_start: 0.7867 (mt) cc_final: 0.7644 (mt) REVERT: E 76 ASN cc_start: 0.6340 (p0) cc_final: 0.6001 (p0) REVERT: E 212 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8372 (pp) REVERT: E 301 LYS cc_start: 0.8710 (ttpp) cc_final: 0.8468 (ttpp) REVERT: F 76 ASN cc_start: 0.6366 (p0) cc_final: 0.6111 (p0) REVERT: F 277 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7565 (mm110) REVERT: G 76 ASN cc_start: 0.6387 (p0) cc_final: 0.6157 (p0) REVERT: H 76 ASN cc_start: 0.6463 (p0) cc_final: 0.6165 (p0) REVERT: H 277 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7272 (mm110) REVERT: I 71 ILE cc_start: 0.8816 (mt) cc_final: 0.8614 (mt) REVERT: I 76 ASN cc_start: 0.6460 (p0) cc_final: 0.5968 (p0) REVERT: I 301 LYS cc_start: 0.8953 (ttpp) cc_final: 0.8709 (ttpt) REVERT: J 76 ASN cc_start: 0.6577 (p0) cc_final: 0.6260 (p0) outliers start: 33 outliers final: 25 residues processed: 349 average time/residue: 0.2906 time to fit residues: 164.6933 Evaluate side-chains 280 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 254 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 195 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 5.9990 chunk 216 optimal weight: 0.0870 chunk 120 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 224 optimal weight: 0.0020 chunk 86 optimal weight: 7.9990 chunk 136 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 259 optimal weight: 0.9980 overall best weight: 0.7768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 246 ASN A 300 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN B 246 ASN B 300 HIS C 246 ASN C 277 GLN C 300 HIS D 246 ASN D 300 HIS E 246 ASN E 257 ASN E 300 HIS F 246 ASN F 300 HIS G 216 GLN G 246 ASN G 300 HIS H 216 GLN H 246 ASN H 300 HIS I 246 ASN I 300 HIS J 216 GLN J 246 ASN J 277 GLN J 300 HIS K 216 GLN K 246 ASN K 300 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23067 Z= 0.213 Angle : 0.714 8.332 31526 Z= 0.378 Chirality : 0.040 0.114 3520 Planarity : 0.006 0.043 4048 Dihedral : 6.713 53.742 3231 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.27 % Allowed : 17.50 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.14), residues: 2871 helix: -1.32 (0.11), residues: 1815 sheet: None (None), residues: 0 loop : -2.99 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 220 HIS 0.005 0.001 HIS G 238 PHE 0.016 0.001 PHE D 250 TYR 0.017 0.002 TYR I 285 ARG 0.003 0.000 ARG D 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 290 time to evaluate : 2.127 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: A 78 HIS cc_start: 0.7527 (t-90) cc_final: 0.6757 (t-90) REVERT: A 81 ASN cc_start: 0.7850 (m-40) cc_final: 0.7512 (t0) REVERT: A 181 ARG cc_start: 0.7044 (mmm160) cc_final: 0.6402 (mmt180) REVERT: A 262 GLU cc_start: 0.7507 (pp20) cc_final: 0.6585 (pp20) REVERT: A 266 ASN cc_start: 0.7640 (m-40) cc_final: 0.6772 (m110) REVERT: B 81 ASN cc_start: 0.7761 (m-40) cc_final: 0.7160 (t0) REVERT: B 200 PHE cc_start: 0.7839 (t80) cc_final: 0.7548 (t80) REVERT: B 262 GLU cc_start: 0.7217 (pp20) cc_final: 0.6729 (pp20) REVERT: B 266 ASN cc_start: 0.7858 (m-40) cc_final: 0.7573 (m-40) REVERT: B 277 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7236 (tt0) REVERT: C 81 ASN cc_start: 0.7692 (m-40) cc_final: 0.7357 (t0) REVERT: C 262 GLU cc_start: 0.7457 (pp20) cc_final: 0.6883 (pp20) REVERT: C 266 ASN cc_start: 0.7732 (m-40) cc_final: 0.7344 (m110) REVERT: D 81 ASN cc_start: 0.7468 (m-40) cc_final: 0.6980 (t0) REVERT: D 198 LEU cc_start: 0.7889 (tp) cc_final: 0.7599 (tp) REVERT: D 262 GLU cc_start: 0.7663 (pp20) cc_final: 0.7434 (pp20) REVERT: D 277 GLN cc_start: 0.7404 (mm110) cc_final: 0.7194 (tt0) REVERT: D 284 VAL cc_start: 0.6862 (OUTLIER) cc_final: 0.6618 (m) REVERT: D 293 LEU cc_start: 0.7743 (mt) cc_final: 0.7539 (mt) REVERT: E 81 ASN cc_start: 0.7747 (m-40) cc_final: 0.7288 (t0) REVERT: E 212 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8132 (pp) REVERT: E 277 GLN cc_start: 0.7517 (mm110) cc_final: 0.7174 (tt0) REVERT: E 301 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8420 (ttpt) REVERT: F 81 ASN cc_start: 0.7551 (m-40) cc_final: 0.7320 (t0) REVERT: F 200 PHE cc_start: 0.7864 (t80) cc_final: 0.7435 (t80) REVERT: F 277 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7297 (tt0) REVERT: G 78 HIS cc_start: 0.7315 (t-90) cc_final: 0.6807 (t-90) REVERT: G 81 ASN cc_start: 0.7941 (m-40) cc_final: 0.7478 (t0) REVERT: G 277 GLN cc_start: 0.7672 (mm110) cc_final: 0.7166 (tt0) REVERT: H 78 HIS cc_start: 0.7846 (t-90) cc_final: 0.7280 (t-90) REVERT: H 81 ASN cc_start: 0.7694 (m-40) cc_final: 0.7250 (t0) REVERT: I 81 ASN cc_start: 0.7495 (m-40) cc_final: 0.7272 (t0) REVERT: I 277 GLN cc_start: 0.7737 (mm110) cc_final: 0.7323 (tt0) REVERT: I 301 LYS cc_start: 0.9035 (ttpp) cc_final: 0.8724 (ttpt) REVERT: J 81 ASN cc_start: 0.7809 (m-40) cc_final: 0.7517 (t0) REVERT: J 200 PHE cc_start: 0.7622 (t80) cc_final: 0.7394 (t80) REVERT: J 266 ASN cc_start: 0.7526 (m-40) cc_final: 0.7323 (m-40) REVERT: J 284 VAL cc_start: 0.6374 (OUTLIER) cc_final: 0.6120 (m) REVERT: K 81 ASN cc_start: 0.7870 (m-40) cc_final: 0.7635 (t0) outliers start: 72 outliers final: 46 residues processed: 348 average time/residue: 0.2889 time to fit residues: 163.5825 Evaluate side-chains 296 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 247 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 228 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 228 ASP Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 228 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 144 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 216 optimal weight: 3.9990 chunk 176 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 260 optimal weight: 20.0000 chunk 281 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 208 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN C 216 GLN D 216 GLN D 277 GLN E 87 GLN E 216 GLN F 87 GLN F 216 GLN G 87 GLN G 266 ASN G 277 GLN H 216 GLN I 216 GLN I 266 ASN ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 GLN K 216 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23067 Z= 0.194 Angle : 0.641 8.060 31526 Z= 0.328 Chirality : 0.039 0.122 3520 Planarity : 0.005 0.060 4048 Dihedral : 5.754 49.203 3220 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.36 % Allowed : 17.55 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.16), residues: 2871 helix: 0.21 (0.12), residues: 1826 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 189 HIS 0.004 0.001 HIS J 88 PHE 0.021 0.001 PHE B 250 TYR 0.020 0.001 TYR G 285 ARG 0.007 0.000 ARG I 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 279 time to evaluate : 2.455 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: A 78 HIS cc_start: 0.7664 (t-90) cc_final: 0.6948 (t-90) REVERT: A 81 ASN cc_start: 0.7791 (m-40) cc_final: 0.7486 (t0) REVERT: A 181 ARG cc_start: 0.7246 (mmm160) cc_final: 0.6604 (mmt180) REVERT: A 262 GLU cc_start: 0.7329 (pp20) cc_final: 0.6666 (pp20) REVERT: A 266 ASN cc_start: 0.7848 (m-40) cc_final: 0.7176 (m-40) REVERT: A 269 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7760 (m) REVERT: B 81 ASN cc_start: 0.7751 (m-40) cc_final: 0.7185 (t0) REVERT: B 262 GLU cc_start: 0.7195 (pp20) cc_final: 0.6715 (pp20) REVERT: B 266 ASN cc_start: 0.7684 (m-40) cc_final: 0.7434 (m-40) REVERT: B 277 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7165 (tt0) REVERT: C 78 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.7625 (t-90) REVERT: C 81 ASN cc_start: 0.7626 (m-40) cc_final: 0.7194 (t0) REVERT: C 157 LEU cc_start: 0.5466 (OUTLIER) cc_final: 0.5070 (pp) REVERT: C 262 GLU cc_start: 0.7302 (pp20) cc_final: 0.6787 (pp20) REVERT: C 266 ASN cc_start: 0.7694 (m-40) cc_final: 0.7190 (m-40) REVERT: D 81 ASN cc_start: 0.7548 (m-40) cc_final: 0.7281 (t0) REVERT: D 270 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6476 (tm-30) REVERT: D 293 LEU cc_start: 0.7738 (mt) cc_final: 0.7530 (mt) REVERT: E 78 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7487 (t-90) REVERT: E 81 ASN cc_start: 0.7908 (m-40) cc_final: 0.7371 (t0) REVERT: E 204 CYS cc_start: 0.7659 (m) cc_final: 0.7240 (t) REVERT: E 212 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8281 (pp) REVERT: E 277 GLN cc_start: 0.7460 (mm110) cc_final: 0.7114 (tt0) REVERT: E 301 LYS cc_start: 0.8638 (ttpp) cc_final: 0.8379 (ttpt) REVERT: F 78 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7688 (t-90) REVERT: F 81 ASN cc_start: 0.7964 (m-40) cc_final: 0.7566 (t0) REVERT: F 200 PHE cc_start: 0.7822 (t80) cc_final: 0.7497 (t80) REVERT: F 277 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7177 (tt0) REVERT: G 78 HIS cc_start: 0.7486 (t-90) cc_final: 0.6827 (t-90) REVERT: G 81 ASN cc_start: 0.8037 (m-40) cc_final: 0.7593 (t0) REVERT: G 277 GLN cc_start: 0.7602 (mm-40) cc_final: 0.7186 (tt0) REVERT: H 78 HIS cc_start: 0.7794 (t-90) cc_final: 0.7179 (t-90) REVERT: H 81 ASN cc_start: 0.7760 (m-40) cc_final: 0.7317 (t0) REVERT: H 233 ARG cc_start: 0.7360 (ttm170) cc_final: 0.7041 (ttp-110) REVERT: H 262 GLU cc_start: 0.7524 (pp20) cc_final: 0.7283 (pp20) REVERT: I 78 HIS cc_start: 0.7331 (t-90) cc_final: 0.6529 (t-90) REVERT: I 204 CYS cc_start: 0.7948 (m) cc_final: 0.7559 (t) REVERT: I 261 GLU cc_start: 0.7320 (tp30) cc_final: 0.7072 (tp30) REVERT: I 262 GLU cc_start: 0.7615 (pp20) cc_final: 0.6884 (pp20) REVERT: I 266 ASN cc_start: 0.7925 (m-40) cc_final: 0.7544 (m-40) REVERT: I 277 GLN cc_start: 0.7682 (mm110) cc_final: 0.7171 (tt0) REVERT: I 301 LYS cc_start: 0.9028 (ttpp) cc_final: 0.8643 (ttpp) REVERT: J 78 HIS cc_start: 0.8055 (OUTLIER) cc_final: 0.7521 (t-90) REVERT: J 81 ASN cc_start: 0.7770 (m-40) cc_final: 0.7372 (t0) REVERT: J 200 PHE cc_start: 0.7670 (t80) cc_final: 0.7269 (t80) REVERT: J 269 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7683 (m) REVERT: J 270 GLU cc_start: 0.6228 (tt0) cc_final: 0.6010 (tt0) REVERT: K 78 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7771 (t-90) REVERT: K 81 ASN cc_start: 0.8084 (m-40) cc_final: 0.7793 (t0) outliers start: 96 outliers final: 47 residues processed: 343 average time/residue: 0.2715 time to fit residues: 154.6546 Evaluate side-chains 305 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 248 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 228 ASP Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 228 ASP Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 78 HIS Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 257 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 261 optimal weight: 20.0000 chunk 276 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 ASN C 152 HIS D 277 GLN E 216 GLN H 87 GLN I 87 GLN I 216 GLN J 279 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23067 Z= 0.337 Angle : 0.707 8.607 31526 Z= 0.361 Chirality : 0.043 0.139 3520 Planarity : 0.005 0.048 4048 Dihedral : 5.730 46.497 3220 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 4.41 % Allowed : 18.59 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2871 helix: 0.39 (0.12), residues: 1848 sheet: None (None), residues: 0 loop : -2.75 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 220 HIS 0.007 0.001 HIS G 238 PHE 0.013 0.002 PHE C 172 TYR 0.018 0.002 TYR K 287 ARG 0.006 0.000 ARG I 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 269 time to evaluate : 2.307 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: A 78 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.7231 (t-90) REVERT: A 81 ASN cc_start: 0.7944 (m-40) cc_final: 0.7626 (t0) REVERT: A 262 GLU cc_start: 0.7522 (pp20) cc_final: 0.6631 (pp20) REVERT: A 266 ASN cc_start: 0.7831 (m-40) cc_final: 0.7062 (m110) REVERT: B 81 ASN cc_start: 0.7890 (m-40) cc_final: 0.7424 (t0) REVERT: B 200 PHE cc_start: 0.7731 (t80) cc_final: 0.7438 (t80) REVERT: B 262 GLU cc_start: 0.7346 (pp20) cc_final: 0.6856 (pp20) REVERT: B 266 ASN cc_start: 0.7850 (m-40) cc_final: 0.7645 (m-40) REVERT: B 277 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7285 (tt0) REVERT: C 78 HIS cc_start: 0.7812 (OUTLIER) cc_final: 0.7205 (t-90) REVERT: C 81 ASN cc_start: 0.7623 (m-40) cc_final: 0.7327 (t0) REVERT: C 157 LEU cc_start: 0.5450 (OUTLIER) cc_final: 0.5026 (pp) REVERT: C 262 GLU cc_start: 0.7590 (pp20) cc_final: 0.7192 (pp20) REVERT: D 78 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.7127 (t-90) REVERT: D 81 ASN cc_start: 0.7615 (m-40) cc_final: 0.7360 (t0) REVERT: D 270 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6191 (tm-30) REVERT: E 78 HIS cc_start: 0.7877 (t-90) cc_final: 0.7426 (t-90) REVERT: E 212 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8141 (pp) REVERT: E 262 GLU cc_start: 0.7377 (pp20) cc_final: 0.7164 (pp20) REVERT: E 277 GLN cc_start: 0.7552 (mm110) cc_final: 0.7196 (tt0) REVERT: E 301 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8407 (ttpt) REVERT: F 78 HIS cc_start: 0.8030 (t-90) cc_final: 0.7677 (t-90) REVERT: F 81 ASN cc_start: 0.7920 (m-40) cc_final: 0.7617 (t0) REVERT: F 200 PHE cc_start: 0.7826 (t80) cc_final: 0.7544 (t80) REVERT: F 277 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7244 (tt0) REVERT: G 78 HIS cc_start: 0.7324 (OUTLIER) cc_final: 0.7108 (t-90) REVERT: G 81 ASN cc_start: 0.8098 (m-40) cc_final: 0.7671 (t0) REVERT: G 277 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7253 (tt0) REVERT: H 78 HIS cc_start: 0.7778 (OUTLIER) cc_final: 0.7206 (t-90) REVERT: H 81 ASN cc_start: 0.7969 (m-40) cc_final: 0.7598 (t0) REVERT: H 233 ARG cc_start: 0.7608 (ttm170) cc_final: 0.7360 (ttp-110) REVERT: I 78 HIS cc_start: 0.7733 (t-90) cc_final: 0.6965 (t-90) REVERT: I 81 ASN cc_start: 0.7977 (OUTLIER) cc_final: 0.7601 (t0) REVERT: I 262 GLU cc_start: 0.7601 (pp20) cc_final: 0.7149 (pp20) REVERT: I 277 GLN cc_start: 0.7733 (mm110) cc_final: 0.7240 (tt0) REVERT: I 301 LYS cc_start: 0.9090 (ttpp) cc_final: 0.8783 (tttm) REVERT: J 78 HIS cc_start: 0.7988 (t-90) cc_final: 0.7565 (t-90) REVERT: J 81 ASN cc_start: 0.7825 (m-40) cc_final: 0.7428 (t0) REVERT: J 200 PHE cc_start: 0.7641 (t80) cc_final: 0.7238 (t80) REVERT: J 270 GLU cc_start: 0.6401 (tt0) cc_final: 0.6184 (tt0) REVERT: K 78 HIS cc_start: 0.7885 (t-90) cc_final: 0.7538 (t-90) REVERT: K 81 ASN cc_start: 0.8160 (m-40) cc_final: 0.7911 (t0) outliers start: 97 outliers final: 67 residues processed: 338 average time/residue: 0.2895 time to fit residues: 159.6058 Evaluate side-chains 331 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 255 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 81 ASN Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 228 ASP Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 230 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN C 266 ASN D 87 GLN G 290 ASN J 87 GLN ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 23067 Z= 0.317 Angle : 0.698 8.893 31526 Z= 0.351 Chirality : 0.042 0.133 3520 Planarity : 0.005 0.044 4048 Dihedral : 5.592 44.414 3220 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 4.86 % Allowed : 20.05 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2871 helix: 0.59 (0.12), residues: 1848 sheet: None (None), residues: 0 loop : -2.65 (0.21), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 220 HIS 0.007 0.001 HIS G 238 PHE 0.011 0.001 PHE K 69 TYR 0.017 0.002 TYR I 285 ARG 0.003 0.000 ARG I 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 264 time to evaluate : 2.599 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: A 78 HIS cc_start: 0.8003 (OUTLIER) cc_final: 0.7616 (t-90) REVERT: A 81 ASN cc_start: 0.7929 (m-40) cc_final: 0.7572 (t0) REVERT: A 262 GLU cc_start: 0.7488 (pp20) cc_final: 0.6573 (pp20) REVERT: A 266 ASN cc_start: 0.7890 (m-40) cc_final: 0.7088 (m110) REVERT: B 78 HIS cc_start: 0.7896 (OUTLIER) cc_final: 0.7254 (t-90) REVERT: B 81 ASN cc_start: 0.7826 (m-40) cc_final: 0.7346 (t0) REVERT: B 200 PHE cc_start: 0.7738 (t80) cc_final: 0.7493 (t80) REVERT: B 262 GLU cc_start: 0.7341 (pp20) cc_final: 0.6828 (pp20) REVERT: B 266 ASN cc_start: 0.7922 (m-40) cc_final: 0.7679 (m-40) REVERT: C 78 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7330 (t-90) REVERT: C 81 ASN cc_start: 0.7652 (m-40) cc_final: 0.7345 (t0) REVERT: C 157 LEU cc_start: 0.5476 (OUTLIER) cc_final: 0.5088 (pp) REVERT: C 262 GLU cc_start: 0.7592 (pp20) cc_final: 0.7197 (pp20) REVERT: D 78 HIS cc_start: 0.7572 (OUTLIER) cc_final: 0.7222 (t-90) REVERT: D 81 ASN cc_start: 0.7627 (m-40) cc_final: 0.7371 (t0) REVERT: D 270 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.6129 (tm-30) REVERT: E 81 ASN cc_start: 0.7578 (t0) cc_final: 0.7025 (t0) REVERT: E 212 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8023 (pp) REVERT: E 277 GLN cc_start: 0.7554 (mm110) cc_final: 0.7197 (tt0) REVERT: E 301 LYS cc_start: 0.8756 (ttpp) cc_final: 0.8522 (ttpt) REVERT: F 78 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7651 (t-90) REVERT: F 81 ASN cc_start: 0.7944 (m-40) cc_final: 0.7688 (t0) REVERT: F 277 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7264 (tt0) REVERT: G 78 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.7265 (t-90) REVERT: G 81 ASN cc_start: 0.8111 (m-40) cc_final: 0.7689 (t0) REVERT: G 181 ARG cc_start: 0.7606 (mmm-85) cc_final: 0.7327 (mmt90) REVERT: G 277 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7153 (tt0) REVERT: H 78 HIS cc_start: 0.7841 (OUTLIER) cc_final: 0.7500 (t-90) REVERT: H 81 ASN cc_start: 0.7974 (m-40) cc_final: 0.7594 (t0) REVERT: H 262 GLU cc_start: 0.7498 (pp20) cc_final: 0.7177 (pp20) REVERT: I 78 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7479 (t-90) REVERT: I 81 ASN cc_start: 0.7939 (OUTLIER) cc_final: 0.7517 (t0) REVERT: I 262 GLU cc_start: 0.7634 (pp20) cc_final: 0.7272 (pp20) REVERT: I 277 GLN cc_start: 0.7718 (mm110) cc_final: 0.7178 (tt0) REVERT: I 301 LYS cc_start: 0.9083 (ttpp) cc_final: 0.8793 (tttm) REVERT: J 78 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7577 (t-90) REVERT: J 81 ASN cc_start: 0.7800 (m-40) cc_final: 0.7382 (t0) REVERT: J 200 PHE cc_start: 0.7713 (t80) cc_final: 0.7261 (t80) REVERT: K 78 HIS cc_start: 0.8038 (OUTLIER) cc_final: 0.7692 (t-90) outliers start: 107 outliers final: 63 residues processed: 333 average time/residue: 0.2857 time to fit residues: 157.0590 Evaluate side-chains 330 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 253 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 78 HIS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 78 HIS Chi-restraints excluded: chain I residue 81 ASN Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 228 ASP Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 281 ILE Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 78 HIS Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 93 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 276 optimal weight: 0.7980 chunk 229 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN C 266 ASN E 290 ASN I 266 ASN ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 23067 Z= 0.294 Angle : 0.688 9.553 31526 Z= 0.345 Chirality : 0.042 0.131 3520 Planarity : 0.005 0.062 4048 Dihedral : 5.491 42.217 3220 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 5.14 % Allowed : 20.77 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.17), residues: 2871 helix: 0.67 (0.12), residues: 1881 sheet: None (None), residues: 0 loop : -2.79 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 189 HIS 0.006 0.001 HIS G 238 PHE 0.010 0.001 PHE C 172 TYR 0.018 0.002 TYR I 285 ARG 0.004 0.000 ARG C 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 261 time to evaluate : 2.272 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: A 78 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7644 (t-90) REVERT: A 81 ASN cc_start: 0.7924 (m-40) cc_final: 0.7557 (t0) REVERT: A 262 GLU cc_start: 0.7367 (pp20) cc_final: 0.6673 (pp20) REVERT: A 266 ASN cc_start: 0.7907 (m-40) cc_final: 0.7328 (m-40) REVERT: B 78 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.7302 (t-90) REVERT: B 81 ASN cc_start: 0.7856 (m-40) cc_final: 0.7386 (t0) REVERT: B 200 PHE cc_start: 0.7722 (t80) cc_final: 0.7493 (t80) REVERT: B 262 GLU cc_start: 0.7337 (pp20) cc_final: 0.6798 (pp20) REVERT: B 266 ASN cc_start: 0.7904 (m-40) cc_final: 0.7648 (m-40) REVERT: C 81 ASN cc_start: 0.7662 (m-40) cc_final: 0.7383 (t0) REVERT: C 157 LEU cc_start: 0.5182 (OUTLIER) cc_final: 0.4938 (pp) REVERT: C 262 GLU cc_start: 0.7608 (pp20) cc_final: 0.7118 (pp20) REVERT: D 78 HIS cc_start: 0.7639 (OUTLIER) cc_final: 0.7252 (t-90) REVERT: D 81 ASN cc_start: 0.7569 (m-40) cc_final: 0.7304 (t0) REVERT: D 270 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6149 (tm-30) REVERT: E 78 HIS cc_start: 0.7773 (t-90) cc_final: 0.7291 (t-90) REVERT: E 81 ASN cc_start: 0.7510 (m-40) cc_final: 0.7083 (t0) REVERT: E 212 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8075 (pp) REVERT: E 277 GLN cc_start: 0.7537 (mm110) cc_final: 0.7190 (tt0) REVERT: E 301 LYS cc_start: 0.8761 (ttpp) cc_final: 0.8528 (ttpt) REVERT: F 78 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7667 (t-90) REVERT: F 81 ASN cc_start: 0.7951 (m-40) cc_final: 0.7683 (t0) REVERT: F 277 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7268 (tt0) REVERT: G 78 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.7519 (t-90) REVERT: G 81 ASN cc_start: 0.8105 (m-40) cc_final: 0.7663 (t0) REVERT: G 181 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.7281 (mmt90) REVERT: G 277 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7143 (tt0) REVERT: H 78 HIS cc_start: 0.7859 (OUTLIER) cc_final: 0.7597 (t-90) REVERT: H 81 ASN cc_start: 0.7980 (m-40) cc_final: 0.7576 (t0) REVERT: H 262 GLU cc_start: 0.7548 (pp20) cc_final: 0.7232 (pp20) REVERT: I 75 LEU cc_start: 0.7702 (tt) cc_final: 0.7453 (tp) REVERT: I 78 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.7506 (t-90) REVERT: I 81 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7538 (t0) REVERT: I 277 GLN cc_start: 0.7704 (mm110) cc_final: 0.7132 (tt0) REVERT: I 301 LYS cc_start: 0.9052 (ttpp) cc_final: 0.8759 (tttm) REVERT: J 78 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7518 (t-90) REVERT: J 200 PHE cc_start: 0.7719 (t80) cc_final: 0.7297 (t80) REVERT: J 236 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6423 (tp30) REVERT: K 78 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7734 (t-90) REVERT: K 256 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8125 (mt) outliers start: 113 outliers final: 69 residues processed: 336 average time/residue: 0.2695 time to fit residues: 150.7161 Evaluate side-chains 342 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 258 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 78 HIS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 78 HIS Chi-restraints excluded: chain I residue 81 ASN Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 228 ASP Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 78 HIS Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 266 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 chunk 202 optimal weight: 0.5980 chunk 156 optimal weight: 9.9990 chunk 232 optimal weight: 1.9990 chunk 154 optimal weight: 0.0770 chunk 275 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 ASN G 290 ASN I 266 ASN ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23067 Z= 0.225 Angle : 0.656 8.661 31526 Z= 0.326 Chirality : 0.041 0.135 3520 Planarity : 0.004 0.041 4048 Dihedral : 5.198 40.119 3219 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.18 % Allowed : 22.14 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2871 helix: 0.93 (0.12), residues: 1881 sheet: None (None), residues: 0 loop : -2.68 (0.22), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 189 HIS 0.004 0.001 HIS G 238 PHE 0.008 0.001 PHE A 69 TYR 0.023 0.001 TYR B 285 ARG 0.005 0.000 ARG D 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 266 time to evaluate : 2.504 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: A 78 HIS cc_start: 0.8064 (OUTLIER) cc_final: 0.7682 (t-90) REVERT: A 81 ASN cc_start: 0.7945 (m-40) cc_final: 0.7618 (t0) REVERT: A 262 GLU cc_start: 0.7308 (pp20) cc_final: 0.6617 (pp20) REVERT: A 266 ASN cc_start: 0.7853 (m-40) cc_final: 0.7307 (m-40) REVERT: A 269 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7647 (m) REVERT: B 78 HIS cc_start: 0.7934 (OUTLIER) cc_final: 0.7342 (t-90) REVERT: B 81 ASN cc_start: 0.7788 (m-40) cc_final: 0.7434 (t0) REVERT: B 262 GLU cc_start: 0.7284 (pp20) cc_final: 0.6693 (pp20) REVERT: B 266 ASN cc_start: 0.7852 (m-40) cc_final: 0.7577 (m-40) REVERT: C 78 HIS cc_start: 0.7704 (OUTLIER) cc_final: 0.7129 (t-90) REVERT: C 81 ASN cc_start: 0.7749 (m-40) cc_final: 0.7434 (t0) REVERT: C 262 GLU cc_start: 0.7411 (pp20) cc_final: 0.7137 (pp20) REVERT: D 78 HIS cc_start: 0.7821 (OUTLIER) cc_final: 0.7440 (t-90) REVERT: D 81 ASN cc_start: 0.7614 (m-40) cc_final: 0.7352 (t0) REVERT: D 270 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5949 (tm-30) REVERT: E 81 ASN cc_start: 0.7790 (m-40) cc_final: 0.7442 (t0) REVERT: E 212 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7891 (pp) REVERT: E 277 GLN cc_start: 0.7464 (mm110) cc_final: 0.7133 (tt0) REVERT: E 301 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8506 (tttm) REVERT: F 78 HIS cc_start: 0.8039 (OUTLIER) cc_final: 0.7771 (t-90) REVERT: F 81 ASN cc_start: 0.7916 (m-40) cc_final: 0.7555 (t0) REVERT: F 277 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7255 (tt0) REVERT: G 81 ASN cc_start: 0.8100 (m-40) cc_final: 0.7644 (t0) REVERT: G 277 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7207 (tt0) REVERT: H 78 HIS cc_start: 0.8000 (OUTLIER) cc_final: 0.7641 (t-90) REVERT: H 81 ASN cc_start: 0.7970 (m-40) cc_final: 0.7552 (t0) REVERT: H 262 GLU cc_start: 0.7518 (pp20) cc_final: 0.7149 (pp20) REVERT: I 78 HIS cc_start: 0.7989 (OUTLIER) cc_final: 0.7581 (t-90) REVERT: I 81 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7544 (t0) REVERT: I 262 GLU cc_start: 0.7589 (pp20) cc_final: 0.7177 (pp20) REVERT: I 277 GLN cc_start: 0.7661 (mm110) cc_final: 0.7092 (tt0) REVERT: I 301 LYS cc_start: 0.8968 (ttpp) cc_final: 0.8674 (tttm) REVERT: J 78 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.7536 (t-90) REVERT: J 81 ASN cc_start: 0.7841 (t0) cc_final: 0.7409 (t0) REVERT: J 200 PHE cc_start: 0.7584 (t80) cc_final: 0.7206 (t80) REVERT: J 269 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7543 (m) REVERT: K 78 HIS cc_start: 0.8031 (OUTLIER) cc_final: 0.7630 (t-90) REVERT: K 81 ASN cc_start: 0.8206 (t0) cc_final: 0.7257 (t0) outliers start: 92 outliers final: 56 residues processed: 324 average time/residue: 0.2793 time to fit residues: 149.4755 Evaluate side-chains 318 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 248 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 78 HIS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 228 ASP Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 78 HIS Chi-restraints excluded: chain I residue 81 ASN Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 228 ASP Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 78 HIS Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 170 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 164 optimal weight: 0.0370 chunk 83 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 175 optimal weight: 0.9980 chunk 187 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 25 optimal weight: 0.1980 chunk 216 optimal weight: 5.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS E 78 HIS G 290 ASN H 88 HIS H 216 GLN I 266 ASN ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23067 Z= 0.178 Angle : 0.647 9.934 31526 Z= 0.314 Chirality : 0.040 0.169 3520 Planarity : 0.004 0.041 4048 Dihedral : 4.983 39.242 3219 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 3.59 % Allowed : 23.23 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2871 helix: 1.27 (0.12), residues: 1881 sheet: None (None), residues: 0 loop : -2.61 (0.22), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 189 HIS 0.009 0.001 HIS H 88 PHE 0.013 0.001 PHE B 200 TYR 0.025 0.001 TYR E 285 ARG 0.004 0.000 ARG D 179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 272 time to evaluate : 2.413 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: A 78 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.7690 (t-90) REVERT: A 81 ASN cc_start: 0.7896 (m-40) cc_final: 0.7538 (t0) REVERT: A 262 GLU cc_start: 0.7362 (pp20) cc_final: 0.6682 (pp20) REVERT: A 266 ASN cc_start: 0.7823 (m-40) cc_final: 0.7327 (m-40) REVERT: A 269 VAL cc_start: 0.7960 (OUTLIER) cc_final: 0.7624 (m) REVERT: B 78 HIS cc_start: 0.7814 (OUTLIER) cc_final: 0.7199 (t-90) REVERT: B 81 ASN cc_start: 0.7709 (m-40) cc_final: 0.7351 (t0) REVERT: B 262 GLU cc_start: 0.7178 (pp20) cc_final: 0.6452 (pp20) REVERT: B 266 ASN cc_start: 0.7912 (m-40) cc_final: 0.7554 (m-40) REVERT: C 78 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.7211 (t-90) REVERT: C 81 ASN cc_start: 0.7797 (m-40) cc_final: 0.7487 (t0) REVERT: D 66 LEU cc_start: 0.7647 (tp) cc_final: 0.7304 (mp) REVERT: D 78 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.7401 (t-90) REVERT: D 81 ASN cc_start: 0.7628 (m-40) cc_final: 0.7343 (t0) REVERT: D 270 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.6220 (tm-30) REVERT: E 81 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7369 (t0) REVERT: E 204 CYS cc_start: 0.7548 (m) cc_final: 0.7282 (t) REVERT: E 212 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8132 (pp) REVERT: E 277 GLN cc_start: 0.7529 (mm110) cc_final: 0.7109 (tt0) REVERT: E 301 LYS cc_start: 0.8826 (ttpp) cc_final: 0.8558 (tttm) REVERT: F 78 HIS cc_start: 0.8004 (OUTLIER) cc_final: 0.7756 (t-90) REVERT: F 81 ASN cc_start: 0.7881 (m-40) cc_final: 0.7585 (t0) REVERT: F 198 LEU cc_start: 0.8140 (tp) cc_final: 0.7761 (tp) REVERT: F 262 GLU cc_start: 0.7678 (pp20) cc_final: 0.7356 (pp20) REVERT: F 266 ASN cc_start: 0.8004 (m-40) cc_final: 0.7741 (m110) REVERT: F 277 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7162 (tt0) REVERT: G 78 HIS cc_start: 0.7835 (t-90) cc_final: 0.7380 (t-90) REVERT: G 81 ASN cc_start: 0.7949 (m-40) cc_final: 0.7552 (t0) REVERT: G 269 VAL cc_start: 0.7710 (OUTLIER) cc_final: 0.7471 (m) REVERT: G 277 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7240 (tt0) REVERT: H 78 HIS cc_start: 0.8003 (OUTLIER) cc_final: 0.7596 (t-90) REVERT: H 81 ASN cc_start: 0.7930 (m-40) cc_final: 0.7475 (t0) REVERT: H 262 GLU cc_start: 0.7482 (pp20) cc_final: 0.7135 (pp20) REVERT: H 269 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7562 (m) REVERT: I 78 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7586 (t-90) REVERT: I 81 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7465 (t0) REVERT: I 204 CYS cc_start: 0.7759 (m) cc_final: 0.7523 (t) REVERT: I 262 GLU cc_start: 0.7586 (pp20) cc_final: 0.7168 (pp20) REVERT: I 277 GLN cc_start: 0.7521 (mm110) cc_final: 0.7001 (tt0) REVERT: I 301 LYS cc_start: 0.8874 (ttpp) cc_final: 0.8536 (tttm) REVERT: J 78 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.7588 (t-90) REVERT: J 81 ASN cc_start: 0.7633 (t0) cc_final: 0.7116 (t0) REVERT: J 200 PHE cc_start: 0.7341 (t80) cc_final: 0.7015 (t80) REVERT: J 236 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6297 (tp30) REVERT: J 261 GLU cc_start: 0.7253 (tp30) cc_final: 0.7022 (tp30) REVERT: J 269 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7639 (m) REVERT: K 78 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7699 (t-90) REVERT: K 81 ASN cc_start: 0.8147 (t0) cc_final: 0.7260 (t0) REVERT: K 204 CYS cc_start: 0.7700 (m) cc_final: 0.7432 (t) outliers start: 79 outliers final: 49 residues processed: 314 average time/residue: 0.2834 time to fit residues: 148.5104 Evaluate side-chains 329 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 262 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 78 HIS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 228 ASP Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 88 HIS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 78 HIS Chi-restraints excluded: chain I residue 81 ASN Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 228 ASP Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 78 HIS Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 250 optimal weight: 0.8980 chunk 264 optimal weight: 0.9990 chunk 240 optimal weight: 0.7980 chunk 256 optimal weight: 0.0000 chunk 154 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 201 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 242 optimal weight: 0.9990 chunk 255 optimal weight: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS B 88 HIS ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 HIS G 266 ASN H 88 HIS J 216 GLN ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23067 Z= 0.180 Angle : 0.643 8.933 31526 Z= 0.312 Chirality : 0.039 0.114 3520 Planarity : 0.004 0.043 4048 Dihedral : 4.881 38.798 3219 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.36 % Allowed : 23.82 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2871 helix: 1.49 (0.12), residues: 1881 sheet: None (None), residues: 0 loop : -2.61 (0.22), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 189 HIS 0.018 0.001 HIS H 88 PHE 0.009 0.001 PHE I 250 TYR 0.026 0.001 TYR I 285 ARG 0.006 0.000 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 270 time to evaluate : 2.474 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: A 78 HIS cc_start: 0.8149 (OUTLIER) cc_final: 0.7884 (t-90) REVERT: A 81 ASN cc_start: 0.7868 (m-40) cc_final: 0.7478 (t0) REVERT: A 262 GLU cc_start: 0.7367 (pp20) cc_final: 0.6966 (pp20) REVERT: A 266 ASN cc_start: 0.7806 (m-40) cc_final: 0.7536 (m-40) REVERT: A 269 VAL cc_start: 0.7975 (OUTLIER) cc_final: 0.7637 (m) REVERT: B 78 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7215 (t-90) REVERT: B 81 ASN cc_start: 0.7663 (m-40) cc_final: 0.7284 (t0) REVERT: B 262 GLU cc_start: 0.7229 (pp20) cc_final: 0.6500 (pp20) REVERT: B 266 ASN cc_start: 0.7828 (m-40) cc_final: 0.7453 (m-40) REVERT: C 78 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7223 (t-90) REVERT: C 81 ASN cc_start: 0.7629 (m-40) cc_final: 0.7319 (t0) REVERT: D 66 LEU cc_start: 0.7721 (tp) cc_final: 0.7453 (mp) REVERT: D 78 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.7405 (t-90) REVERT: D 81 ASN cc_start: 0.7694 (m-40) cc_final: 0.7332 (t0) REVERT: D 270 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6355 (tm-30) REVERT: E 81 ASN cc_start: 0.7707 (m-40) cc_final: 0.7374 (t0) REVERT: E 204 CYS cc_start: 0.7453 (m) cc_final: 0.7226 (t) REVERT: E 212 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8139 (pp) REVERT: E 277 GLN cc_start: 0.7450 (mm110) cc_final: 0.7032 (tt0) REVERT: E 301 LYS cc_start: 0.8822 (ttpp) cc_final: 0.8529 (ttpt) REVERT: F 78 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7857 (t-90) REVERT: F 81 ASN cc_start: 0.7890 (m-40) cc_final: 0.7611 (t0) REVERT: F 198 LEU cc_start: 0.8127 (tp) cc_final: 0.7746 (tp) REVERT: F 277 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7161 (tt0) REVERT: G 78 HIS cc_start: 0.7932 (t-90) cc_final: 0.7498 (t70) REVERT: G 81 ASN cc_start: 0.7941 (m-40) cc_final: 0.7541 (t0) REVERT: G 277 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7321 (tt0) REVERT: H 78 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.7622 (t-90) REVERT: H 81 ASN cc_start: 0.7938 (m-40) cc_final: 0.7493 (t0) REVERT: H 262 GLU cc_start: 0.7511 (pp20) cc_final: 0.7185 (pp20) REVERT: H 269 VAL cc_start: 0.7939 (OUTLIER) cc_final: 0.7704 (m) REVERT: H 270 GLU cc_start: 0.5861 (tt0) cc_final: 0.5591 (tt0) REVERT: I 78 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.7732 (t-90) REVERT: I 81 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7442 (t0) REVERT: I 204 CYS cc_start: 0.7737 (m) cc_final: 0.7497 (t) REVERT: I 262 GLU cc_start: 0.7539 (pp20) cc_final: 0.7166 (pp20) REVERT: I 277 GLN cc_start: 0.7538 (mm110) cc_final: 0.7021 (tt0) REVERT: I 301 LYS cc_start: 0.8874 (ttpp) cc_final: 0.8530 (tttm) REVERT: J 78 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.7598 (t-90) REVERT: J 81 ASN cc_start: 0.7643 (t0) cc_final: 0.6993 (t0) REVERT: J 200 PHE cc_start: 0.7356 (t80) cc_final: 0.7050 (t80) REVERT: J 236 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6305 (tp30) REVERT: J 261 GLU cc_start: 0.7272 (tp30) cc_final: 0.7023 (tp30) REVERT: J 269 VAL cc_start: 0.7970 (OUTLIER) cc_final: 0.7649 (m) REVERT: K 78 HIS cc_start: 0.8201 (OUTLIER) cc_final: 0.7807 (t-90) REVERT: K 81 ASN cc_start: 0.8159 (t0) cc_final: 0.7099 (t0) REVERT: K 204 CYS cc_start: 0.7718 (m) cc_final: 0.7465 (t) outliers start: 74 outliers final: 50 residues processed: 312 average time/residue: 0.2853 time to fit residues: 148.7345 Evaluate side-chains 324 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 258 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 78 HIS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 88 HIS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 78 HIS Chi-restraints excluded: chain I residue 81 ASN Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 228 ASP Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 78 HIS Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 168 optimal weight: 0.0770 chunk 271 optimal weight: 7.9990 chunk 165 optimal weight: 0.9980 chunk 128 optimal weight: 0.0570 chunk 188 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 226 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 139 optimal weight: 0.2980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 HIS H 88 HIS I 88 HIS J 88 HIS ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23067 Z= 0.176 Angle : 0.641 8.740 31526 Z= 0.310 Chirality : 0.039 0.132 3520 Planarity : 0.004 0.043 4048 Dihedral : 4.813 38.830 3219 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.14 % Allowed : 24.59 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2871 helix: 1.59 (0.12), residues: 1903 sheet: None (None), residues: 0 loop : -2.70 (0.22), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 189 HIS 0.014 0.001 HIS H 88 PHE 0.010 0.001 PHE I 250 TYR 0.023 0.001 TYR I 285 ARG 0.006 0.000 ARG B 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 259 time to evaluate : 2.412 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: A 78 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7778 (t-90) REVERT: A 81 ASN cc_start: 0.7906 (m-40) cc_final: 0.7530 (t0) REVERT: A 262 GLU cc_start: 0.7382 (pp20) cc_final: 0.7007 (pp20) REVERT: A 266 ASN cc_start: 0.7792 (m-40) cc_final: 0.7507 (m-40) REVERT: A 269 VAL cc_start: 0.7838 (OUTLIER) cc_final: 0.7490 (m) REVERT: B 78 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.7315 (t-90) REVERT: B 81 ASN cc_start: 0.7610 (m-40) cc_final: 0.7224 (t0) REVERT: B 262 GLU cc_start: 0.7111 (pp20) cc_final: 0.6733 (pp20) REVERT: C 78 HIS cc_start: 0.7677 (OUTLIER) cc_final: 0.7144 (t-90) REVERT: C 81 ASN cc_start: 0.7604 (m-40) cc_final: 0.7290 (t0) REVERT: C 261 GLU cc_start: 0.7515 (tp30) cc_final: 0.7271 (tp30) REVERT: D 66 LEU cc_start: 0.7647 (tp) cc_final: 0.7395 (mp) REVERT: D 78 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.7349 (t-90) REVERT: D 81 ASN cc_start: 0.7699 (m-40) cc_final: 0.7325 (t0) REVERT: D 270 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6216 (tm-30) REVERT: E 81 ASN cc_start: 0.7648 (m-40) cc_final: 0.7323 (t0) REVERT: E 212 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8004 (pp) REVERT: E 277 GLN cc_start: 0.7471 (mm110) cc_final: 0.7052 (tt0) REVERT: E 301 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8517 (ttpt) REVERT: F 78 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7826 (t-90) REVERT: F 81 ASN cc_start: 0.7956 (m-40) cc_final: 0.7600 (t0) REVERT: F 198 LEU cc_start: 0.8106 (tp) cc_final: 0.7738 (tp) REVERT: F 262 GLU cc_start: 0.7631 (pp20) cc_final: 0.7326 (pp20) REVERT: F 266 ASN cc_start: 0.7964 (m-40) cc_final: 0.7722 (m110) REVERT: F 277 GLN cc_start: 0.7354 (mm-40) cc_final: 0.7108 (tt0) REVERT: G 78 HIS cc_start: 0.8110 (t-90) cc_final: 0.7594 (t70) REVERT: G 81 ASN cc_start: 0.7915 (m-40) cc_final: 0.7509 (t0) REVERT: G 277 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7370 (tt0) REVERT: H 78 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7637 (t-90) REVERT: H 81 ASN cc_start: 0.7949 (m-40) cc_final: 0.7555 (t0) REVERT: H 204 CYS cc_start: 0.7781 (m) cc_final: 0.7333 (t) REVERT: H 262 GLU cc_start: 0.7485 (pp20) cc_final: 0.7191 (pp20) REVERT: H 270 GLU cc_start: 0.5795 (tt0) cc_final: 0.5519 (tt0) REVERT: I 78 HIS cc_start: 0.8120 (OUTLIER) cc_final: 0.7733 (t-90) REVERT: I 81 ASN cc_start: 0.7823 (t0) cc_final: 0.7376 (t0) REVERT: I 262 GLU cc_start: 0.7539 (pp20) cc_final: 0.7165 (pp20) REVERT: I 277 GLN cc_start: 0.7505 (mm110) cc_final: 0.6998 (tt0) REVERT: I 301 LYS cc_start: 0.8858 (ttpp) cc_final: 0.8521 (tttm) REVERT: J 78 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7577 (t-90) REVERT: J 81 ASN cc_start: 0.7643 (t0) cc_final: 0.6954 (t0) REVERT: J 82 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8977 (tp) REVERT: J 200 PHE cc_start: 0.7361 (t80) cc_final: 0.7081 (t80) REVERT: J 236 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6287 (tp30) REVERT: J 261 GLU cc_start: 0.7253 (tp30) cc_final: 0.6999 (tp30) REVERT: J 269 VAL cc_start: 0.7897 (OUTLIER) cc_final: 0.7585 (m) REVERT: K 78 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7804 (t-90) REVERT: K 81 ASN cc_start: 0.8100 (t0) cc_final: 0.7033 (t0) REVERT: K 204 CYS cc_start: 0.7633 (m) cc_final: 0.7422 (t) outliers start: 69 outliers final: 49 residues processed: 300 average time/residue: 0.2786 time to fit residues: 139.5064 Evaluate side-chains 313 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 249 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 78 HIS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 228 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 88 HIS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 78 HIS Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 228 ASP Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 78 HIS Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 180 optimal weight: 0.9980 chunk 241 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 227 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 28 optimal weight: 0.2980 chunk 41 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 HIS E 88 HIS F 88 HIS G 88 HIS H 88 HIS H 277 GLN J 257 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.257105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.172964 restraints weight = 24741.865| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 3.29 r_work: 0.3551 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23067 Z= 0.230 Angle : 0.659 8.473 31526 Z= 0.323 Chirality : 0.041 0.116 3520 Planarity : 0.004 0.040 4048 Dihedral : 4.857 38.128 3219 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.36 % Allowed : 25.05 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2871 helix: 1.52 (0.12), residues: 1903 sheet: None (None), residues: 0 loop : -2.71 (0.22), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 189 HIS 0.018 0.001 HIS H 88 PHE 0.009 0.001 PHE F 69 TYR 0.018 0.001 TYR I 285 ARG 0.004 0.000 ARG B 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4382.17 seconds wall clock time: 79 minutes 53.09 seconds (4793.09 seconds total)