Starting phenix.real_space_refine on Fri Feb 16 21:44:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/02_2024/6lqh_0945.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/02_2024/6lqh_0945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/02_2024/6lqh_0945.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/02_2024/6lqh_0945.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/02_2024/6lqh_0945.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/02_2024/6lqh_0945.pdb" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 54 5.16 5 C 10503 2.51 5 N 2853 2.21 5 O 3213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 210": "OD1" <-> "OD2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 210": "OD1" <-> "OD2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 58": "OD1" <-> "OD2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 210": "OD1" <-> "OD2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 58": "OD1" <-> "OD2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 210": "OD1" <-> "OD2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 58": "OD1" <-> "OD2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 210": "OD1" <-> "OD2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 58": "OD1" <-> "OD2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 210": "OD1" <-> "OD2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 210": "OD1" <-> "OD2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "H PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 58": "OD1" <-> "OD2" Residue "I GLU 59": "OE1" <-> "OE2" Residue "I TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 91": "NH1" <-> "NH2" Residue "I PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 210": "OD1" <-> "OD2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16623 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "B" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "C" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "D" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "E" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "F" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "G" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "H" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "I" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "a" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "b" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "d" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "e" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "g" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "h" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "i" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 8.75, per 1000 atoms: 0.53 Number of scatterers: 16623 At special positions: 0 Unit cell: (112, 111, 115, 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 54 16.00 O 3213 8.00 N 2853 7.00 C 10503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.21 Conformation dependent library (CDL) restraints added in 3.1 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 26.2% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 81 through 90 Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 226 through 249 Processing helix chain 'B' and resid 81 through 90 Processing helix chain 'B' and resid 100 through 115 Processing helix chain 'B' and resid 226 through 249 Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 226 through 249 Processing helix chain 'D' and resid 81 through 90 Processing helix chain 'D' and resid 100 through 115 Processing helix chain 'D' and resid 226 through 249 Processing helix chain 'E' and resid 81 through 90 Processing helix chain 'E' and resid 100 through 115 Processing helix chain 'E' and resid 226 through 249 Processing helix chain 'F' and resid 81 through 90 Processing helix chain 'F' and resid 100 through 115 Processing helix chain 'F' and resid 226 through 249 Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 100 through 115 Processing helix chain 'G' and resid 226 through 249 Processing helix chain 'H' and resid 81 through 90 Processing helix chain 'H' and resid 100 through 115 Processing helix chain 'H' and resid 226 through 249 Processing helix chain 'I' and resid 81 through 90 Processing helix chain 'I' and resid 100 through 115 Processing helix chain 'I' and resid 226 through 249 Processing helix chain 'a' and resid 35 through 47 removed outlier: 4.334A pdb=" N ALA a 39 " --> pdb=" O PRO a 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE a 40 " --> pdb=" O ASN a 36 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 47 removed outlier: 4.335A pdb=" N ALA b 39 " --> pdb=" O PRO b 35 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE b 40 " --> pdb=" O ASN b 36 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 47 removed outlier: 4.334A pdb=" N ALA c 39 " --> pdb=" O PRO c 35 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE c 40 " --> pdb=" O ASN c 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 47 removed outlier: 4.335A pdb=" N ALA d 39 " --> pdb=" O PRO d 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE d 40 " --> pdb=" O ASN d 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 35 through 47 removed outlier: 4.335A pdb=" N ALA e 39 " --> pdb=" O PRO e 35 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE e 40 " --> pdb=" O ASN e 36 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 47 removed outlier: 4.334A pdb=" N ALA f 39 " --> pdb=" O PRO f 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE f 40 " --> pdb=" O ASN f 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 47 removed outlier: 4.334A pdb=" N ALA g 39 " --> pdb=" O PRO g 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE g 40 " --> pdb=" O ASN g 36 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 47 removed outlier: 4.335A pdb=" N ALA h 39 " --> pdb=" O PRO h 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE h 40 " --> pdb=" O ASN h 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 47 removed outlier: 4.335A pdb=" N ALA i 39 " --> pdb=" O PRO i 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE i 40 " --> pdb=" O ASN i 36 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN A 57 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY A 144 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL A 149 " --> pdb=" O ASN B 224 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 207 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE B 186 " --> pdb=" O ASN B 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN B 180 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 163 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY B 155 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR B 165 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY B 153 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR B 167 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER B 151 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 169 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN B 171 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER B 147 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA B 173 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR B 145 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN B 175 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE B 143 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG B 177 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER B 141 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 179 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU B 139 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 136 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 52 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE B 49 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU B 96 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 51 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN B 57 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY B 144 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL B 149 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG E 213 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG E 207 " --> pdb=" O LEU E 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE E 186 " --> pdb=" O ASN E 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN E 180 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA E 163 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY E 155 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR E 165 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY E 153 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR E 167 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER E 151 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU E 169 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN E 171 " --> pdb=" O SER E 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER E 147 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA E 173 " --> pdb=" O TYR E 145 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR E 145 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN E 175 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE E 143 " --> pdb=" O ASN E 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG E 177 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER E 141 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL E 179 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU E 139 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE E 136 " --> pdb=" O PHE E 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER E 52 " --> pdb=" O ILE E 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN E 57 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY E 144 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL E 149 " --> pdb=" O ASN H 224 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG H 213 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG H 207 " --> pdb=" O LEU H 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE H 186 " --> pdb=" O ASN H 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN H 180 " --> pdb=" O ILE H 186 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA H 163 " --> pdb=" O GLY H 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY H 155 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR H 165 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY H 153 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR H 167 " --> pdb=" O SER H 151 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER H 151 " --> pdb=" O TYR H 167 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU H 169 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN H 171 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER H 147 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA H 173 " --> pdb=" O TYR H 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR H 145 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN H 175 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE H 143 " --> pdb=" O ASN H 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG H 177 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER H 141 " --> pdb=" O ARG H 177 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL H 179 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU H 139 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE H 136 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER H 52 " --> pdb=" O ILE H 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 56 through 57 removed outlier: 7.099A pdb=" N GLN H 57 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY H 144 " --> pdb=" O GLN H 57 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL H 149 " --> pdb=" O ASN F 224 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG F 213 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG F 207 " --> pdb=" O LEU F 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE F 186 " --> pdb=" O ASN F 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN F 180 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA F 163 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY F 155 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR F 165 " --> pdb=" O GLY F 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY F 153 " --> pdb=" O THR F 165 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR F 167 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER F 151 " --> pdb=" O TYR F 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU F 169 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN F 171 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER F 147 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA F 173 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR F 145 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN F 175 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE F 143 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ARG F 177 " --> pdb=" O SER F 141 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N SER F 141 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL F 179 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU F 139 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE F 136 " --> pdb=" O PHE F 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER F 52 " --> pdb=" O ILE F 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN F 57 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY F 144 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL F 149 " --> pdb=" O ASN D 224 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG D 207 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE D 186 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASN D 180 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA D 163 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY D 155 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR D 165 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY D 153 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR D 167 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER D 151 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU D 169 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN D 171 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER D 147 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA D 173 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR D 145 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN D 175 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE D 143 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG D 177 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER D 141 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL D 179 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU D 139 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE D 136 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 52 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN D 57 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY D 144 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL D 149 " --> pdb=" O ASN C 224 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 207 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE C 186 " --> pdb=" O ASN C 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN C 180 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA C 163 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY C 155 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR C 165 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY C 153 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR C 167 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER C 151 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU C 169 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN C 171 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER C 147 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA C 173 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR C 145 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN C 175 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE C 143 " --> pdb=" O ASN C 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG C 177 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N SER C 141 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 179 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU C 139 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE C 136 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 52 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE C 49 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU C 96 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 51 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN C 57 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY C 144 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL C 149 " --> pdb=" O ASN G 224 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG G 213 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG G 207 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE G 186 " --> pdb=" O ASN G 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN G 180 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA G 163 " --> pdb=" O GLY G 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY G 155 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR G 165 " --> pdb=" O GLY G 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY G 153 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR G 167 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER G 151 " --> pdb=" O TYR G 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU G 169 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN G 171 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER G 147 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA G 173 " --> pdb=" O TYR G 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR G 145 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN G 175 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE G 143 " --> pdb=" O ASN G 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG G 177 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER G 141 " --> pdb=" O ARG G 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL G 179 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU G 139 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE G 136 " --> pdb=" O PHE G 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER G 52 " --> pdb=" O ILE G 136 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE G 49 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU G 96 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL G 51 " --> pdb=" O LEU G 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN G 57 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY G 144 " --> pdb=" O GLN G 57 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL G 149 " --> pdb=" O ASN I 224 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG I 213 " --> pdb=" O ILE I 209 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG I 207 " --> pdb=" O LEU I 215 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE I 186 " --> pdb=" O ASN I 180 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASN I 180 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA I 163 " --> pdb=" O GLY I 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY I 155 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR I 165 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY I 153 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR I 167 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER I 151 " --> pdb=" O TYR I 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU I 169 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN I 171 " --> pdb=" O SER I 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER I 147 " --> pdb=" O GLN I 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA I 173 " --> pdb=" O TYR I 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR I 145 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN I 175 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE I 143 " --> pdb=" O ASN I 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG I 177 " --> pdb=" O SER I 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER I 141 " --> pdb=" O ARG I 177 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL I 179 " --> pdb=" O GLU I 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU I 139 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE I 136 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER I 52 " --> pdb=" O ILE I 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 56 through 57 removed outlier: 7.099A pdb=" N GLN I 57 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY I 144 " --> pdb=" O GLN I 57 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL I 149 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 207 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE A 186 " --> pdb=" O ASN A 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN A 180 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA A 163 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY A 155 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR A 165 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY A 153 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR A 167 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER A 151 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 169 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN A 171 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N SER A 147 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA A 173 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR A 145 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN A 175 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE A 143 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ARG A 177 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER A 141 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 179 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU A 139 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 136 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 52 " --> pdb=" O ILE A 136 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2295 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: 5.29 Time building geometry restraints manager: 6.79 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: 5597 1.34 - 1.45: 2474 1.45 - 1.57: 8732 1.57 - 1.68: 0 1.68 - 1.80: 99 Bond restraints: 16902 Sorted by residual: bond pdb=" CG PRO C 67 " pdb=" CD PRO C 67 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.17e+00 bond pdb=" CG PRO H 67 " pdb=" CD PRO H 67 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.17e+00 bond pdb=" CG PRO I 67 " pdb=" CD PRO I 67 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.14e+00 bond pdb=" CG PRO G 67 " pdb=" CD PRO G 67 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.14e+00 bond pdb=" CG PRO D 67 " pdb=" CD PRO D 67 " ideal model delta sigma weight residual 1.512 1.473 0.039 2.70e-02 1.37e+03 2.10e+00 ... (remaining 16897 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.43: 361 106.43 - 113.41: 9089 113.41 - 120.39: 6846 120.39 - 127.37: 6517 127.37 - 134.35: 110 Bond angle restraints: 22923 Sorted by residual: angle pdb=" N GLY d 33 " pdb=" CA GLY d 33 " pdb=" C GLY d 33 " ideal model delta sigma weight residual 113.18 121.91 -8.73 2.37e+00 1.78e-01 1.36e+01 angle pdb=" N GLY g 33 " pdb=" CA GLY g 33 " pdb=" C GLY g 33 " ideal model delta sigma weight residual 113.18 121.89 -8.71 2.37e+00 1.78e-01 1.35e+01 angle pdb=" N GLY f 33 " pdb=" CA GLY f 33 " pdb=" C GLY f 33 " ideal model delta sigma weight residual 113.18 121.88 -8.70 2.37e+00 1.78e-01 1.35e+01 angle pdb=" N GLY a 33 " pdb=" CA GLY a 33 " pdb=" C GLY a 33 " ideal model delta sigma weight residual 113.18 121.88 -8.70 2.37e+00 1.78e-01 1.35e+01 angle pdb=" N GLY h 33 " pdb=" CA GLY h 33 " pdb=" C GLY h 33 " ideal model delta sigma weight residual 113.18 121.87 -8.69 2.37e+00 1.78e-01 1.35e+01 ... (remaining 22918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 8668 15.68 - 31.37: 899 31.37 - 47.05: 243 47.05 - 62.73: 189 62.73 - 78.42: 36 Dihedral angle restraints: 10035 sinusoidal: 3888 harmonic: 6147 Sorted by residual: dihedral pdb=" CA GLN A 99 " pdb=" C GLN A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual -180.00 -152.45 -27.55 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA GLN E 99 " pdb=" C GLN E 99 " pdb=" N GLY E 100 " pdb=" CA GLY E 100 " ideal model delta harmonic sigma weight residual -180.00 -152.45 -27.55 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA GLN H 99 " pdb=" C GLN H 99 " pdb=" N GLY H 100 " pdb=" CA GLY H 100 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 10032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1410 0.037 - 0.074: 842 0.074 - 0.111: 244 0.111 - 0.148: 89 0.148 - 0.185: 16 Chirality restraints: 2601 Sorted by residual: chirality pdb=" CA PHE h 31 " pdb=" N PHE h 31 " pdb=" C PHE h 31 " pdb=" CB PHE h 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA PHE d 31 " pdb=" N PHE d 31 " pdb=" C PHE d 31 " pdb=" CB PHE d 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA PHE c 31 " pdb=" N PHE c 31 " pdb=" C PHE c 31 " pdb=" CB PHE c 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 2598 not shown) Planarity restraints: 3024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE f 31 " 0.014 2.00e-02 2.50e+03 1.31e-02 3.02e+00 pdb=" CG PHE f 31 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE f 31 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE f 31 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE f 31 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE f 31 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE f 31 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE h 31 " 0.014 2.00e-02 2.50e+03 1.31e-02 3.00e+00 pdb=" CG PHE h 31 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE h 31 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE h 31 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE h 31 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE h 31 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE h 31 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE b 31 " -0.014 2.00e-02 2.50e+03 1.30e-02 2.98e+00 pdb=" CG PHE b 31 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE b 31 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE b 31 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE b 31 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE b 31 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE b 31 " -0.002 2.00e-02 2.50e+03 ... (remaining 3021 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4554 2.79 - 3.32: 15055 3.32 - 3.85: 29376 3.85 - 4.37: 35899 4.37 - 4.90: 62728 Nonbonded interactions: 147612 Sorted by model distance: nonbonded pdb=" O SER e 50 " pdb=" OG SER e 50 " model vdw 2.268 2.440 nonbonded pdb=" O SER f 50 " pdb=" OG SER f 50 " model vdw 2.268 2.440 nonbonded pdb=" O SER d 50 " pdb=" OG SER d 50 " model vdw 2.269 2.440 nonbonded pdb=" O SER b 50 " pdb=" OG SER b 50 " model vdw 2.269 2.440 nonbonded pdb=" O SER c 50 " pdb=" OG SER c 50 " model vdw 2.269 2.440 ... (remaining 147607 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' } 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' } 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.550 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 44.470 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 16902 Z= 0.543 Angle : 0.825 8.734 22923 Z= 0.461 Chirality : 0.051 0.185 2601 Planarity : 0.004 0.027 3024 Dihedral : 17.093 78.418 6111 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 9.05 % Allowed : 11.56 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.73 (0.16), residues: 2124 helix: -1.15 (0.17), residues: 576 sheet: -0.81 (0.21), residues: 666 loop : -3.05 (0.16), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 252 PHE 0.031 0.002 PHE f 31 TYR 0.013 0.002 TYR E 158 ARG 0.003 0.001 ARG c 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 427 time to evaluate : 1.975 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8917 (mttp) cc_final: 0.8704 (mttt) REVERT: A 109 LYS cc_start: 0.8794 (mttp) cc_final: 0.8560 (mttt) REVERT: A 232 MET cc_start: 0.7953 (tpt) cc_final: 0.7439 (tpt) REVERT: B 70 ASN cc_start: 0.8423 (m-40) cc_final: 0.8151 (m-40) REVERT: B 170 ASP cc_start: 0.8106 (m-30) cc_final: 0.7904 (m-30) REVERT: C 48 LYS cc_start: 0.8463 (mttt) cc_final: 0.8263 (mttt) REVERT: C 70 ASN cc_start: 0.8420 (m-40) cc_final: 0.8018 (m-40) REVERT: C 166 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: C 185 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7557 (pt0) REVERT: D 70 ASN cc_start: 0.8450 (m-40) cc_final: 0.8060 (m-40) REVERT: D 88 LYS cc_start: 0.8891 (tptp) cc_final: 0.8677 (tptm) REVERT: D 109 LYS cc_start: 0.8838 (mttp) cc_final: 0.8537 (mtmt) REVERT: D 137 MET cc_start: 0.8463 (ttm) cc_final: 0.8125 (ttp) REVERT: D 141 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8909 (p) REVERT: D 166 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: D 170 ASP cc_start: 0.8182 (m-30) cc_final: 0.7972 (m-30) REVERT: E 109 LYS cc_start: 0.8863 (mttp) cc_final: 0.8661 (mttp) REVERT: E 166 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: E 170 ASP cc_start: 0.8193 (m-30) cc_final: 0.7934 (m-30) REVERT: E 185 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: F 70 ASN cc_start: 0.8410 (m-40) cc_final: 0.8143 (m110) REVERT: F 102 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7772 (tp40) REVERT: F 137 MET cc_start: 0.8380 (ttm) cc_final: 0.8083 (ttp) REVERT: F 141 SER cc_start: 0.9180 (OUTLIER) cc_final: 0.8898 (p) REVERT: F 166 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: F 213 ARG cc_start: 0.8306 (mmt-90) cc_final: 0.7918 (mmt180) REVERT: F 240 ILE cc_start: 0.8779 (mt) cc_final: 0.8549 (mp) REVERT: G 59 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7540 (mt-10) REVERT: G 88 LYS cc_start: 0.8909 (tptp) cc_final: 0.8581 (mtpp) REVERT: G 109 LYS cc_start: 0.8799 (mttp) cc_final: 0.8527 (mttt) REVERT: G 166 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: H 59 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7642 (mt-10) REVERT: H 109 LYS cc_start: 0.8825 (mttp) cc_final: 0.8595 (mttt) REVERT: H 141 SER cc_start: 0.9145 (OUTLIER) cc_final: 0.8942 (p) REVERT: H 185 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: H 193 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8467 (t) REVERT: H 200 GLU cc_start: 0.7820 (tt0) cc_final: 0.7604 (tt0) REVERT: I 64 LYS cc_start: 0.8904 (mttp) cc_final: 0.8660 (mttt) REVERT: I 70 ASN cc_start: 0.8486 (m-40) cc_final: 0.8273 (m110) REVERT: I 88 LYS cc_start: 0.8909 (tptp) cc_final: 0.8596 (mtpp) REVERT: I 109 LYS cc_start: 0.8795 (mttp) cc_final: 0.8573 (mttp) REVERT: I 167 TYR cc_start: 0.8685 (p90) cc_final: 0.8439 (p90) REVERT: I 185 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7516 (pt0) REVERT: e 44 SER cc_start: 0.8427 (p) cc_final: 0.8191 (p) REVERT: h 44 SER cc_start: 0.8536 (p) cc_final: 0.8317 (p) outliers start: 162 outliers final: 57 residues processed: 559 average time/residue: 1.3611 time to fit residues: 839.2024 Evaluate side-chains 376 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 306 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 252 TRP Chi-restraints excluded: chain a residue 50 SER Chi-restraints excluded: chain b residue 50 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain d residue 50 SER Chi-restraints excluded: chain e residue 50 SER Chi-restraints excluded: chain f residue 50 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain h residue 50 SER Chi-restraints excluded: chain i residue 50 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 30.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 148 ASN A 171 GLN A 212 GLN B 62 GLN B 148 ASN B 244 ASN C 62 GLN C 171 GLN D 62 GLN D 77 GLN D 148 ASN D 171 GLN E 62 GLN E 77 GLN E 148 ASN E 171 GLN F 62 GLN F 148 ASN F 171 GLN F 212 GLN G 62 GLN G 70 ASN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN H 62 GLN H 168 GLN I 62 GLN I 77 GLN I 171 GLN a 43 ASN b 43 ASN c 43 ASN d 43 ASN e 43 ASN f 43 ASN g 43 ASN h 43 ASN i 43 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16902 Z= 0.206 Angle : 0.650 7.974 22923 Z= 0.337 Chirality : 0.046 0.143 2601 Planarity : 0.003 0.025 3024 Dihedral : 8.925 89.225 2422 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.52 % Allowed : 19.88 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.39 (0.17), residues: 2124 helix: 0.83 (0.20), residues: 585 sheet: -0.55 (0.22), residues: 612 loop : -2.38 (0.16), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 92 PHE 0.018 0.001 PHE d 31 TYR 0.009 0.001 TYR C 199 ARG 0.005 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 314 time to evaluate : 1.949 Fit side-chains revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8583 (t80) cc_final: 0.8298 (t80) REVERT: B 70 ASN cc_start: 0.8258 (m-40) cc_final: 0.7990 (m-40) REVERT: B 146 GLU cc_start: 0.7239 (tp30) cc_final: 0.6983 (mm-30) REVERT: B 170 ASP cc_start: 0.7995 (m-30) cc_final: 0.7794 (m-30) REVERT: B 213 ARG cc_start: 0.8029 (mmt-90) cc_final: 0.7800 (mmt180) REVERT: B 225 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7722 (tt0) REVERT: B 249 ARG cc_start: 0.7267 (ptp90) cc_final: 0.6995 (ptm-80) REVERT: C 59 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7548 (mt-10) REVERT: C 70 ASN cc_start: 0.8232 (m-40) cc_final: 0.7909 (m-40) REVERT: C 166 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: C 249 ARG cc_start: 0.7264 (ptp90) cc_final: 0.6960 (ptm-80) REVERT: D 70 ASN cc_start: 0.8336 (m-40) cc_final: 0.8012 (m-40) REVERT: D 88 LYS cc_start: 0.8721 (tptp) cc_final: 0.8473 (mtpp) REVERT: D 109 LYS cc_start: 0.8689 (mttp) cc_final: 0.8433 (mtmt) REVERT: D 137 MET cc_start: 0.8401 (ttm) cc_final: 0.8043 (ttp) REVERT: D 141 SER cc_start: 0.9204 (OUTLIER) cc_final: 0.8920 (p) REVERT: D 146 GLU cc_start: 0.7443 (tp30) cc_final: 0.7159 (mm-30) REVERT: D 166 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: D 188 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8756 (p) REVERT: D 249 ARG cc_start: 0.7408 (ptt-90) cc_final: 0.6892 (ptm-80) REVERT: E 59 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7396 (mt-10) REVERT: E 166 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: E 170 ASP cc_start: 0.8063 (m-30) cc_final: 0.7844 (m-30) REVERT: E 249 ARG cc_start: 0.7226 (ptp90) cc_final: 0.7015 (ptm-80) REVERT: F 137 MET cc_start: 0.8285 (ttm) cc_final: 0.8007 (ttp) REVERT: F 166 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: F 249 ARG cc_start: 0.7520 (ptt-90) cc_final: 0.7094 (ptm160) REVERT: G 88 LYS cc_start: 0.8761 (tptp) cc_final: 0.8441 (mtpp) REVERT: G 249 ARG cc_start: 0.7256 (ptp90) cc_final: 0.6940 (ptm-80) REVERT: H 59 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7533 (mt-10) REVERT: H 249 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6992 (ptm160) REVERT: I 59 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7544 (mt-10) REVERT: I 161 ILE cc_start: 0.8439 (mp) cc_final: 0.8185 (mp) REVERT: I 249 ARG cc_start: 0.6785 (ptm-80) cc_final: 0.6492 (ptm-80) REVERT: b 44 SER cc_start: 0.8676 (p) cc_final: 0.8369 (p) REVERT: e 44 SER cc_start: 0.8388 (p) cc_final: 0.8163 (p) REVERT: f 44 SER cc_start: 0.8536 (p) cc_final: 0.8232 (p) outliers start: 63 outliers final: 25 residues processed: 366 average time/residue: 1.4904 time to fit residues: 596.9027 Evaluate side-chains 311 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 279 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.1980 chunk 58 optimal weight: 8.9990 chunk 156 optimal weight: 0.2980 chunk 128 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 203 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN B 148 ASN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN D 148 ASN D 166 GLN E 77 GLN F 70 ASN F 77 GLN G 70 ASN H 148 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 16902 Z= 0.336 Angle : 0.669 8.263 22923 Z= 0.345 Chirality : 0.047 0.144 2601 Planarity : 0.004 0.029 3024 Dihedral : 7.977 86.236 2367 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.52 % Allowed : 20.16 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.01 (0.18), residues: 2124 helix: 1.26 (0.21), residues: 585 sheet: -0.38 (0.21), residues: 702 loop : -2.36 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 92 PHE 0.024 0.002 PHE d 31 TYR 0.014 0.001 TYR C 199 ARG 0.004 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 295 time to evaluate : 1.942 Fit side-chains REVERT: A 66 TYR cc_start: 0.8579 (t80) cc_final: 0.8277 (t80) REVERT: A 249 ARG cc_start: 0.7435 (ptt-90) cc_final: 0.7026 (ptm-80) REVERT: B 70 ASN cc_start: 0.8403 (m-40) cc_final: 0.8141 (m-40) REVERT: B 170 ASP cc_start: 0.8105 (m-30) cc_final: 0.7887 (m-30) REVERT: B 207 ARG cc_start: 0.7737 (ptm-80) cc_final: 0.7531 (ptm-80) REVERT: B 213 ARG cc_start: 0.8090 (mmt-90) cc_final: 0.7732 (mmt180) REVERT: B 249 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.7048 (ptm-80) REVERT: C 70 ASN cc_start: 0.8271 (m-40) cc_final: 0.7996 (m-40) REVERT: C 97 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6297 (tm-30) REVERT: C 146 GLU cc_start: 0.7341 (tp30) cc_final: 0.7075 (tp30) REVERT: C 225 GLU cc_start: 0.8018 (tt0) cc_final: 0.7788 (tt0) REVERT: D 70 ASN cc_start: 0.8310 (m-40) cc_final: 0.8024 (m-40) REVERT: D 88 LYS cc_start: 0.8814 (tptp) cc_final: 0.8573 (tptm) REVERT: D 137 MET cc_start: 0.8464 (ttm) cc_final: 0.8023 (ttp) REVERT: D 146 GLU cc_start: 0.7346 (tp30) cc_final: 0.7059 (mm-30) REVERT: D 228 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8539 (ptt) REVERT: D 249 ARG cc_start: 0.7537 (ptt-90) cc_final: 0.7171 (ptm-80) REVERT: E 59 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7435 (mt-10) REVERT: E 170 ASP cc_start: 0.8147 (m-30) cc_final: 0.7858 (m-30) REVERT: F 59 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7636 (mt-10) REVERT: F 137 MET cc_start: 0.8405 (ttm) cc_final: 0.8082 (ttp) REVERT: F 166 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: F 213 ARG cc_start: 0.8149 (mmt180) cc_final: 0.7846 (mmt180) REVERT: F 219 VAL cc_start: 0.8816 (t) cc_final: 0.8477 (p) REVERT: F 249 ARG cc_start: 0.7579 (ptt-90) cc_final: 0.7309 (ptm160) REVERT: G 59 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7645 (mt-10) REVERT: G 88 LYS cc_start: 0.8864 (tptp) cc_final: 0.8484 (mtpp) REVERT: G 97 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: G 146 GLU cc_start: 0.7453 (tp30) cc_final: 0.7154 (mm-30) REVERT: H 249 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7072 (ptm160) REVERT: I 97 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6819 (tm-30) REVERT: e 44 SER cc_start: 0.8352 (p) cc_final: 0.8059 (p) REVERT: f 44 SER cc_start: 0.8489 (p) cc_final: 0.8229 (p) outliers start: 63 outliers final: 34 residues processed: 344 average time/residue: 1.5639 time to fit residues: 586.8003 Evaluate side-chains 306 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 265 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN B 212 GLN C 148 ASN D 148 ASN E 148 ASN F 148 ASN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16902 Z= 0.305 Angle : 0.646 8.821 22923 Z= 0.332 Chirality : 0.047 0.141 2601 Planarity : 0.003 0.028 3024 Dihedral : 7.568 67.978 2350 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.63 % Allowed : 20.94 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.68 (0.18), residues: 2124 helix: 1.64 (0.21), residues: 585 sheet: -0.21 (0.21), residues: 702 loop : -2.23 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 92 PHE 0.022 0.001 PHE d 31 TYR 0.012 0.001 TYR C 199 ARG 0.003 0.000 ARG I 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 285 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8557 (t80) cc_final: 0.8284 (t80) REVERT: A 97 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: A 219 VAL cc_start: 0.8692 (t) cc_final: 0.8390 (p) REVERT: A 249 ARG cc_start: 0.7372 (ptt-90) cc_final: 0.7066 (ptm-80) REVERT: B 70 ASN cc_start: 0.8361 (m-40) cc_final: 0.8112 (m-40) REVERT: B 109 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8374 (mtmt) REVERT: B 170 ASP cc_start: 0.8057 (m-30) cc_final: 0.7823 (m-30) REVERT: B 213 ARG cc_start: 0.8096 (mmt-90) cc_final: 0.7691 (mmt180) REVERT: B 225 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7757 (tt0) REVERT: C 70 ASN cc_start: 0.8249 (m-40) cc_final: 0.7973 (m-40) REVERT: C 97 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6360 (tm-30) REVERT: C 251 LEU cc_start: 0.7309 (mp) cc_final: 0.7064 (mp) REVERT: D 70 ASN cc_start: 0.8311 (m-40) cc_final: 0.8035 (m-40) REVERT: D 88 LYS cc_start: 0.8794 (tptp) cc_final: 0.8566 (tptm) REVERT: D 137 MET cc_start: 0.8393 (ttm) cc_final: 0.7958 (ttp) REVERT: D 146 GLU cc_start: 0.7346 (tp30) cc_final: 0.7098 (mm-30) REVERT: D 228 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8521 (ptt) REVERT: D 249 ARG cc_start: 0.7404 (ptt-90) cc_final: 0.7100 (ptm160) REVERT: E 59 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7521 (mt-10) REVERT: E 166 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: E 170 ASP cc_start: 0.8101 (m-30) cc_final: 0.7803 (m-30) REVERT: E 218 GLU cc_start: 0.7081 (tp30) cc_final: 0.6851 (tp30) REVERT: F 200 GLU cc_start: 0.7709 (tt0) cc_final: 0.7495 (pp20) REVERT: F 213 ARG cc_start: 0.8187 (mmt-90) cc_final: 0.7744 (mmt180) REVERT: F 219 VAL cc_start: 0.8786 (t) cc_final: 0.8440 (p) REVERT: F 249 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7254 (ptm160) REVERT: G 59 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7617 (mt-10) REVERT: G 88 LYS cc_start: 0.8899 (tptp) cc_final: 0.8476 (mtpp) REVERT: G 97 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6935 (tm-30) REVERT: G 146 GLU cc_start: 0.7431 (tp30) cc_final: 0.7113 (mm-30) REVERT: G 218 GLU cc_start: 0.7210 (tt0) cc_final: 0.6991 (tp30) REVERT: G 249 ARG cc_start: 0.7204 (ptp90) cc_final: 0.6964 (ptm-80) REVERT: H 219 VAL cc_start: 0.8574 (t) cc_final: 0.8344 (p) REVERT: H 249 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6989 (ptm160) REVERT: I 97 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6689 (tm-30) outliers start: 65 outliers final: 35 residues processed: 336 average time/residue: 1.5500 time to fit residues: 568.2841 Evaluate side-chains 312 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 268 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 148 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 170 optimal weight: 0.0870 chunk 138 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 179 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN E 148 ASN F 148 ASN G 77 GLN H 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16902 Z= 0.171 Angle : 0.565 8.619 22923 Z= 0.290 Chirality : 0.045 0.180 2601 Planarity : 0.003 0.030 3024 Dihedral : 6.598 55.696 2347 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.63 % Allowed : 22.33 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.13 (0.19), residues: 2124 helix: 2.38 (0.22), residues: 585 sheet: 0.12 (0.21), residues: 693 loop : -2.14 (0.18), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 92 PHE 0.016 0.001 PHE d 31 TYR 0.010 0.001 TYR C 199 ARG 0.005 0.000 ARG I 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 280 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8430 (t80) cc_final: 0.8066 (t80) REVERT: A 249 ARG cc_start: 0.7251 (ptt-90) cc_final: 0.7019 (ptm-80) REVERT: B 70 ASN cc_start: 0.8314 (m-40) cc_final: 0.8109 (m-40) REVERT: B 88 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8243 (tttp) REVERT: B 109 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8366 (mtmt) REVERT: B 213 ARG cc_start: 0.7989 (mmt-90) cc_final: 0.7650 (mmt180) REVERT: C 249 ARG cc_start: 0.6759 (ptm-80) cc_final: 0.6468 (ptm160) REVERT: D 70 ASN cc_start: 0.8256 (m-40) cc_final: 0.8013 (m-40) REVERT: D 109 LYS cc_start: 0.8619 (mttt) cc_final: 0.8322 (mtmt) REVERT: D 137 MET cc_start: 0.8316 (ttm) cc_final: 0.7972 (ttp) REVERT: D 219 VAL cc_start: 0.8745 (t) cc_final: 0.8468 (p) REVERT: E 59 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7300 (mt-10) REVERT: E 166 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: E 170 ASP cc_start: 0.8024 (m-30) cc_final: 0.7791 (m-30) REVERT: E 218 GLU cc_start: 0.7090 (tp30) cc_final: 0.6870 (tp30) REVERT: F 219 VAL cc_start: 0.8740 (t) cc_final: 0.8518 (p) REVERT: G 88 LYS cc_start: 0.8750 (tptp) cc_final: 0.8349 (mtpp) REVERT: G 97 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6682 (tm-30) REVERT: G 109 LYS cc_start: 0.8682 (mtmm) cc_final: 0.8289 (mtmt) REVERT: G 218 GLU cc_start: 0.7147 (tt0) cc_final: 0.6923 (tp30) REVERT: H 249 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6931 (ptm160) REVERT: I 97 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6815 (tm-30) outliers start: 65 outliers final: 24 residues processed: 324 average time/residue: 1.5005 time to fit residues: 531.9657 Evaluate side-chains 282 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 252 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 166 GLN D 148 ASN D 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 16902 Z= 0.447 Angle : 0.710 9.427 22923 Z= 0.373 Chirality : 0.050 0.178 2601 Planarity : 0.004 0.034 3024 Dihedral : 6.672 70.468 2330 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.18 % Allowed : 22.50 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.48 (0.18), residues: 2124 helix: 1.66 (0.21), residues: 585 sheet: 0.12 (0.21), residues: 702 loop : -2.22 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP E 92 PHE 0.027 0.002 PHE d 31 TYR 0.015 0.002 TYR C 158 ARG 0.005 0.001 ARG I 249 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 290 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8542 (t80) cc_final: 0.8223 (t80) REVERT: A 97 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6729 (tm-30) REVERT: A 249 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.7076 (ptm160) REVERT: B 70 ASN cc_start: 0.8431 (m-40) cc_final: 0.8156 (m-40) REVERT: C 70 ASN cc_start: 0.8317 (m-40) cc_final: 0.8053 (m-40) REVERT: C 97 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6525 (tm-30) REVERT: C 146 GLU cc_start: 0.7479 (tp30) cc_final: 0.7188 (tp30) REVERT: C 219 VAL cc_start: 0.8727 (t) cc_final: 0.8437 (p) REVERT: C 251 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.7010 (mp) REVERT: D 70 ASN cc_start: 0.8378 (m-40) cc_final: 0.8069 (m-40) REVERT: D 137 MET cc_start: 0.8441 (ttm) cc_final: 0.8031 (ttp) REVERT: D 213 ARG cc_start: 0.8067 (mmt-90) cc_final: 0.7697 (mmt180) REVERT: D 219 VAL cc_start: 0.8774 (t) cc_final: 0.8491 (p) REVERT: D 228 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8502 (ptt) REVERT: E 59 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7602 (mt-10) REVERT: E 131 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8584 (mp) REVERT: E 166 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: E 170 ASP cc_start: 0.8128 (m-30) cc_final: 0.7883 (m-30) REVERT: F 219 VAL cc_start: 0.8841 (t) cc_final: 0.8557 (p) REVERT: G 59 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7661 (mt-10) REVERT: G 97 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: H 249 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.7058 (ptm160) REVERT: I 97 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6903 (tm-30) outliers start: 57 outliers final: 28 residues processed: 332 average time/residue: 1.6550 time to fit residues: 597.8766 Evaluate side-chains 311 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 273 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 199 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN D 148 ASN D 168 GLN E 148 ASN F 148 ASN H 148 ASN a 43 ASN b 43 ASN c 43 ASN d 43 ASN e 43 ASN f 43 ASN g 43 ASN h 43 ASN i 43 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16902 Z= 0.192 Angle : 0.604 9.249 22923 Z= 0.314 Chirality : 0.045 0.179 2601 Planarity : 0.003 0.031 3024 Dihedral : 6.087 60.801 2330 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.74 % Allowed : 23.51 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.19), residues: 2124 helix: 2.39 (0.22), residues: 585 sheet: 0.43 (0.22), residues: 666 loop : -2.01 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 252 PHE 0.016 0.001 PHE b 31 TYR 0.009 0.001 TYR C 199 ARG 0.007 0.000 ARG I 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 267 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8442 (t80) cc_final: 0.8093 (t80) REVERT: A 97 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6493 (tm-30) REVERT: B 70 ASN cc_start: 0.8339 (m-40) cc_final: 0.8116 (m-40) REVERT: B 109 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8359 (mtmt) REVERT: C 249 ARG cc_start: 0.6848 (ptm-80) cc_final: 0.6498 (ptm160) REVERT: D 70 ASN cc_start: 0.8283 (m-40) cc_final: 0.8019 (m-40) REVERT: D 109 LYS cc_start: 0.8585 (mttt) cc_final: 0.8343 (mtmt) REVERT: D 137 MET cc_start: 0.8340 (ttm) cc_final: 0.7989 (ttp) REVERT: D 219 VAL cc_start: 0.8744 (t) cc_final: 0.8506 (p) REVERT: D 228 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8450 (ptt) REVERT: E 166 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: E 170 ASP cc_start: 0.8054 (m-30) cc_final: 0.7789 (m-30) REVERT: G 59 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7589 (mt-10) REVERT: G 88 LYS cc_start: 0.8847 (tptp) cc_final: 0.8476 (mtpp) REVERT: G 97 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6779 (tm-30) REVERT: G 219 VAL cc_start: 0.8669 (t) cc_final: 0.8432 (p) REVERT: H 249 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6922 (ptm160) REVERT: I 97 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6730 (tm-30) REVERT: I 219 VAL cc_start: 0.8547 (t) cc_final: 0.8313 (p) REVERT: h 22 MET cc_start: 0.7898 (mtt) cc_final: 0.7519 (mtt) outliers start: 49 outliers final: 26 residues processed: 303 average time/residue: 1.5656 time to fit residues: 518.5681 Evaluate side-chains 307 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 274 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16902 Z= 0.238 Angle : 0.612 8.642 22923 Z= 0.319 Chirality : 0.046 0.158 2601 Planarity : 0.004 0.062 3024 Dihedral : 6.096 60.243 2330 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.46 % Allowed : 24.29 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.15 (0.19), residues: 2124 helix: 2.38 (0.21), residues: 585 sheet: 0.56 (0.22), residues: 666 loop : -1.98 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 92 PHE 0.018 0.001 PHE B 159 TYR 0.013 0.001 TYR C 199 ARG 0.007 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 268 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8431 (t80) cc_final: 0.8051 (t80) REVERT: A 97 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6446 (tm-30) REVERT: B 70 ASN cc_start: 0.8373 (m-40) cc_final: 0.8141 (m-40) REVERT: B 109 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8374 (mtmt) REVERT: C 70 ASN cc_start: 0.8222 (m-40) cc_final: 0.7934 (m-40) REVERT: C 219 VAL cc_start: 0.8680 (t) cc_final: 0.8466 (p) REVERT: C 249 ARG cc_start: 0.6835 (ptm-80) cc_final: 0.6498 (ptm160) REVERT: D 70 ASN cc_start: 0.8301 (m-40) cc_final: 0.8028 (m-40) REVERT: D 109 LYS cc_start: 0.8564 (mttt) cc_final: 0.8331 (mtmt) REVERT: D 137 MET cc_start: 0.8373 (ttm) cc_final: 0.7996 (ttp) REVERT: D 219 VAL cc_start: 0.8748 (t) cc_final: 0.8489 (p) REVERT: D 228 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8465 (ptt) REVERT: E 166 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: E 170 ASP cc_start: 0.8053 (m-30) cc_final: 0.7784 (m-30) REVERT: F 59 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7255 (mt-10) REVERT: G 59 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7629 (mt-10) REVERT: G 88 LYS cc_start: 0.8865 (tptp) cc_final: 0.8482 (mtpp) REVERT: G 97 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6833 (tm-30) REVERT: G 219 VAL cc_start: 0.8662 (t) cc_final: 0.8438 (p) REVERT: H 202 GLN cc_start: 0.7920 (mt0) cc_final: 0.7688 (mt0) REVERT: H 225 GLU cc_start: 0.8029 (tt0) cc_final: 0.7573 (tt0) REVERT: H 249 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6919 (ptm160) REVERT: I 97 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6955 (tm-30) REVERT: I 219 VAL cc_start: 0.8575 (t) cc_final: 0.8368 (p) outliers start: 44 outliers final: 28 residues processed: 301 average time/residue: 1.5767 time to fit residues: 517.0193 Evaluate side-chains 299 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 264 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Chi-restraints excluded: chain h residue 44 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 185 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 168 GLN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN H 168 GLN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 16902 Z= 0.420 Angle : 0.702 9.241 22923 Z= 0.366 Chirality : 0.049 0.162 2601 Planarity : 0.004 0.039 3024 Dihedral : 6.724 71.844 2330 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.29 % Allowed : 24.46 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.19), residues: 2124 helix: 1.83 (0.20), residues: 585 sheet: 0.36 (0.22), residues: 702 loop : -2.21 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP F 92 PHE 0.025 0.002 PHE d 31 TYR 0.018 0.002 TYR C 199 ARG 0.007 0.001 ARG I 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 288 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8484 (t80) cc_final: 0.8158 (t80) REVERT: A 97 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: A 207 ARG cc_start: 0.7841 (ptm160) cc_final: 0.7309 (mtp85) REVERT: B 70 ASN cc_start: 0.8439 (m-40) cc_final: 0.8142 (m-40) REVERT: B 218 GLU cc_start: 0.7125 (tp30) cc_final: 0.6809 (tp30) REVERT: C 97 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6506 (tm-30) REVERT: C 146 GLU cc_start: 0.7352 (tp30) cc_final: 0.7146 (tp30) REVERT: C 147 SER cc_start: 0.8976 (t) cc_final: 0.8640 (p) REVERT: C 219 VAL cc_start: 0.8715 (t) cc_final: 0.8490 (p) REVERT: C 225 GLU cc_start: 0.8129 (tt0) cc_final: 0.7820 (tt0) REVERT: C 249 ARG cc_start: 0.6851 (ptm-80) cc_final: 0.6562 (ptm160) REVERT: D 70 ASN cc_start: 0.8348 (m-40) cc_final: 0.8041 (m-40) REVERT: D 137 MET cc_start: 0.8418 (ttm) cc_final: 0.8010 (ttp) REVERT: D 213 ARG cc_start: 0.8087 (mmt-90) cc_final: 0.7719 (mmt180) REVERT: D 219 VAL cc_start: 0.8761 (t) cc_final: 0.8460 (p) REVERT: D 228 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8496 (ptt) REVERT: E 131 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8540 (mp) REVERT: E 166 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: E 170 ASP cc_start: 0.8087 (m-30) cc_final: 0.7836 (m-30) REVERT: E 249 ARG cc_start: 0.6875 (ptm-80) cc_final: 0.6557 (ptm160) REVERT: F 59 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7507 (mt-10) REVERT: F 131 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8337 (mp) REVERT: G 59 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7699 (mt-10) REVERT: G 88 LYS cc_start: 0.8967 (tptp) cc_final: 0.8520 (mtpp) REVERT: G 97 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: H 249 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6920 (ptm160) REVERT: I 97 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6949 (tm-30) REVERT: I 219 VAL cc_start: 0.8603 (t) cc_final: 0.8348 (p) REVERT: I 249 ARG cc_start: 0.6863 (ptm-80) cc_final: 0.6441 (ptm160) outliers start: 41 outliers final: 23 residues processed: 319 average time/residue: 1.6374 time to fit residues: 568.7484 Evaluate side-chains 298 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 266 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Chi-restraints excluded: chain h residue 44 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 164 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN F 180 ASN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16902 Z= 0.284 Angle : 0.650 9.235 22923 Z= 0.337 Chirality : 0.047 0.156 2601 Planarity : 0.004 0.035 3024 Dihedral : 6.539 72.243 2330 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.84 % Allowed : 25.40 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.19), residues: 2124 helix: 2.18 (0.21), residues: 576 sheet: 0.23 (0.22), residues: 729 loop : -2.15 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 92 PHE 0.019 0.001 PHE b 31 TYR 0.014 0.001 TYR B 158 ARG 0.007 0.000 ARG I 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 262 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8466 (t80) cc_final: 0.8124 (t80) REVERT: A 97 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6567 (tm-30) REVERT: A 207 ARG cc_start: 0.7776 (ptm160) cc_final: 0.7264 (mtp85) REVERT: B 70 ASN cc_start: 0.8391 (m-40) cc_final: 0.8132 (m-40) REVERT: B 218 GLU cc_start: 0.7104 (tp30) cc_final: 0.6783 (tp30) REVERT: C 59 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7318 (mp0) REVERT: C 146 GLU cc_start: 0.7314 (tp30) cc_final: 0.7103 (tp30) REVERT: C 147 SER cc_start: 0.8956 (t) cc_final: 0.8602 (p) REVERT: C 219 VAL cc_start: 0.8685 (t) cc_final: 0.8475 (p) REVERT: C 225 GLU cc_start: 0.8138 (tt0) cc_final: 0.7845 (tt0) REVERT: C 249 ARG cc_start: 0.6796 (ptm-80) cc_final: 0.6532 (ptm160) REVERT: D 70 ASN cc_start: 0.8298 (m-40) cc_final: 0.8031 (m-40) REVERT: D 137 MET cc_start: 0.8318 (ttm) cc_final: 0.7966 (ttp) REVERT: D 213 ARG cc_start: 0.8115 (mmt-90) cc_final: 0.7772 (mmt180) REVERT: D 219 VAL cc_start: 0.8753 (t) cc_final: 0.8480 (p) REVERT: D 228 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8546 (ptt) REVERT: E 166 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: E 170 ASP cc_start: 0.8051 (m-30) cc_final: 0.7772 (m-30) REVERT: E 207 ARG cc_start: 0.7670 (ptm160) cc_final: 0.7443 (ptm160) REVERT: E 249 ARG cc_start: 0.6837 (ptm-80) cc_final: 0.6570 (ptm160) REVERT: F 59 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7355 (mt-10) REVERT: G 59 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7685 (mt-10) REVERT: G 88 LYS cc_start: 0.8918 (tptp) cc_final: 0.8516 (mtpp) REVERT: G 97 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6851 (tm-30) REVERT: G 219 VAL cc_start: 0.8629 (t) cc_final: 0.8406 (p) REVERT: H 249 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6942 (ptm160) REVERT: I 97 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6892 (tm-30) REVERT: I 219 VAL cc_start: 0.8591 (t) cc_final: 0.8371 (p) REVERT: I 249 ARG cc_start: 0.6852 (ptm-80) cc_final: 0.6406 (ptm160) REVERT: i 22 MET cc_start: 0.7368 (mtt) cc_final: 0.7160 (mtt) outliers start: 33 outliers final: 25 residues processed: 291 average time/residue: 1.5981 time to fit residues: 506.0875 Evaluate side-chains 288 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 257 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Chi-restraints excluded: chain h residue 44 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 ASN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.140348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.113564 restraints weight = 18310.720| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.35 r_work: 0.3079 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16902 Z= 0.300 Angle : 0.658 9.563 22923 Z= 0.342 Chirality : 0.047 0.154 2601 Planarity : 0.004 0.034 3024 Dihedral : 6.570 74.231 2330 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.01 % Allowed : 25.63 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.11 (0.19), residues: 2124 helix: 2.20 (0.21), residues: 576 sheet: 0.26 (0.22), residues: 729 loop : -2.14 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 92 PHE 0.019 0.001 PHE b 31 TYR 0.015 0.001 TYR F 167 ARG 0.014 0.000 ARG H 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7995.49 seconds wall clock time: 141 minutes 42.77 seconds (8502.77 seconds total)