Starting phenix.real_space_refine on Tue Aug 6 12:41:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/08_2024/6lqh_0945.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/08_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_0945/08_2024/6lqh_0945.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/08_2024/6lqh_0945.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/08_2024/6lqh_0945.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqh_0945/08_2024/6lqh_0945.cif" } 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-5409/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: 9.57, per 1000 atoms: 0.58 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: 6.68 Conformation dependent library (CDL) restraints added in 2.8 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: 1.50 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: 4.56 Time building geometry restraints manager: 7.20 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 3.040 nonbonded pdb=" O SER f 50 " pdb=" OG SER f 50 " model vdw 2.268 3.040 nonbonded pdb=" O SER d 50 " pdb=" OG SER d 50 " model vdw 2.269 3.040 nonbonded pdb=" O SER b 50 " pdb=" OG SER b 50 " model vdw 2.269 3.040 nonbonded pdb=" O SER c 50 " pdb=" OG SER c 50 " model vdw 2.269 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.870 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: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 45.010 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.880 ------------------------------------------------------------------------------- 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 : 1.704 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: 1.3100 time to fit residues: 807.8692 Evaluate side-chains 376 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 306 time to evaluate : 1.927 ------------------------------------------------------------------------------- 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: 3.9990 chunk 53 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 212 GLN B 62 GLN B 148 ASN C 62 GLN D 62 GLN D 77 GLN D 148 ASN E 62 GLN E 148 ASN E 171 GLN F 62 GLN F 77 GLN F 148 ASN F 212 GLN G 62 GLN G 70 ASN G 77 GLN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN H 168 GLN I 62 GLN I 77 GLN I 148 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16902 Z= 0.242 Angle : 0.665 8.040 22923 Z= 0.349 Chirality : 0.047 0.141 2601 Planarity : 0.004 0.024 3024 Dihedral : 9.102 84.655 2422 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.63 % Allowed : 17.76 % Favored : 78.62 % 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: -1.46 (0.17), residues: 2124 helix: 0.75 (0.20), residues: 585 sheet: -0.68 (0.22), residues: 612 loop : -2.34 (0.16), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 92 PHE 0.019 0.001 PHE d 31 TYR 0.010 0.001 TYR C 199 ARG 0.006 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 372 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 307 time to evaluate : 2.088 Fit side-chains REVERT: A 66 TYR cc_start: 0.8591 (t80) cc_final: 0.8311 (t80) REVERT: A 232 MET cc_start: 0.7800 (tpt) cc_final: 0.7584 (tpt) REVERT: B 70 ASN cc_start: 0.8280 (m-40) cc_final: 0.8010 (m-40) REVERT: B 146 GLU cc_start: 0.7301 (tp30) cc_final: 0.7022 (mm-30) REVERT: B 213 ARG cc_start: 0.8040 (mmt-90) cc_final: 0.7763 (mmt180) REVERT: B 249 ARG cc_start: 0.7457 (ptp90) cc_final: 0.7208 (ptp90) REVERT: C 59 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7488 (mt-10) REVERT: C 70 ASN cc_start: 0.8292 (m-40) cc_final: 0.7965 (m-40) REVERT: C 146 GLU cc_start: 0.7273 (tp30) cc_final: 0.7048 (mm-30) REVERT: C 185 GLU cc_start: 0.7795 (tt0) cc_final: 0.7569 (pt0) REVERT: C 249 ARG cc_start: 0.7468 (ptp90) cc_final: 0.7182 (ptp90) REVERT: D 70 ASN cc_start: 0.8347 (m-40) cc_final: 0.8034 (m-40) REVERT: D 88 LYS cc_start: 0.8758 (tptp) cc_final: 0.8495 (mtpp) REVERT: D 137 MET cc_start: 0.8430 (ttm) cc_final: 0.8022 (ttp) REVERT: D 146 GLU cc_start: 0.7425 (tp30) cc_final: 0.7140 (mm-30) REVERT: D 166 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: D 249 ARG cc_start: 0.7503 (ptt-90) cc_final: 0.7140 (ptm-80) REVERT: E 185 GLU cc_start: 0.7764 (tt0) cc_final: 0.7560 (pt0) REVERT: E 249 ARG cc_start: 0.7332 (ptp90) cc_final: 0.7051 (ptm-80) REVERT: F 131 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8120 (mp) REVERT: F 137 MET cc_start: 0.8355 (ttm) cc_final: 0.8143 (ttp) REVERT: F 166 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: F 213 ARG cc_start: 0.8221 (mmt-90) cc_final: 0.7948 (mmt-90) REVERT: F 249 ARG cc_start: 0.7662 (ptt-90) cc_final: 0.7212 (ptm-80) REVERT: G 88 LYS cc_start: 0.8735 (tptp) cc_final: 0.8398 (mtpp) REVERT: H 146 GLU cc_start: 0.7298 (tp30) cc_final: 0.7096 (mm-30) REVERT: H 249 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7080 (ptm-80) REVERT: I 59 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7560 (mt-10) REVERT: b 44 SER cc_start: 0.8693 (p) cc_final: 0.8371 (p) REVERT: e 44 SER cc_start: 0.8413 (p) cc_final: 0.8113 (p) REVERT: f 44 SER cc_start: 0.8549 (p) cc_final: 0.8246 (p) REVERT: h 44 SER cc_start: 0.8410 (p) cc_final: 0.8207 (p) outliers start: 65 outliers final: 28 residues processed: 359 average time/residue: 1.4152 time to fit residues: 558.1193 Evaluate side-chains 310 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 278 time to evaluate : 1.856 ------------------------------------------------------------------------------- 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 188 SER Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU 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 80 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 154 VAL 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 80 THR 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.6451 > 50: distance: 129 - 130: 8.022 distance: 130 - 131: 47.693 distance: 131 - 132: 41.872 distance: 131 - 133: 15.968 distance: 133 - 134: 16.925 distance: 134 - 135: 22.690 distance: 134 - 137: 42.477 distance: 135 - 136: 10.283 distance: 135 - 140: 4.966 distance: 137 - 138: 3.802 distance: 137 - 139: 40.251 distance: 140 - 141: 20.784 distance: 141 - 142: 34.880 distance: 141 - 144: 43.887 distance: 142 - 143: 40.350 distance: 142 - 148: 24.711 distance: 144 - 145: 26.812 distance: 145 - 146: 26.730 distance: 146 - 147: 30.030 distance: 148 - 149: 22.546 distance: 149 - 150: 27.463 distance: 149 - 152: 5.450 distance: 150 - 151: 23.524 distance: 150 - 155: 28.020 distance: 152 - 153: 11.699 distance: 152 - 154: 57.511 distance: 155 - 156: 13.867 distance: 156 - 157: 11.448 distance: 156 - 159: 28.528 distance: 157 - 166: 27.399 distance: 160 - 161: 16.020 distance: 160 - 162: 9.196 distance: 161 - 163: 43.519 distance: 162 - 164: 34.125 distance: 163 - 165: 4.246 distance: 164 - 165: 35.716 distance: 166 - 167: 35.611 distance: 167 - 168: 57.628 distance: 167 - 170: 17.137 distance: 168 - 169: 5.626 distance: 168 - 175: 46.233 distance: 170 - 171: 39.549 distance: 171 - 172: 27.824 distance: 172 - 173: 10.244 distance: 172 - 174: 6.646 distance: 175 - 176: 3.760 distance: 176 - 177: 6.884 distance: 176 - 179: 7.967 distance: 177 - 178: 14.431 distance: 177 - 186: 4.204 distance: 179 - 180: 10.309 distance: 180 - 181: 33.428 distance: 180 - 182: 38.965 distance: 181 - 183: 37.429 distance: 182 - 184: 7.763 distance: 183 - 185: 18.572 distance: 184 - 185: 34.550 distance: 186 - 187: 27.453 distance: 187 - 188: 19.270 distance: 187 - 190: 26.677 distance: 188 - 189: 16.906 distance: 188 - 197: 22.242 distance: 190 - 191: 19.567 distance: 192 - 193: 23.014 distance: 193 - 194: 24.122 distance: 194 - 195: 41.078 distance: 194 - 196: 39.350 distance: 198 - 201: 24.530 distance: 199 - 200: 19.108 distance: 199 - 205: 34.562 distance: 201 - 202: 22.364 distance: 202 - 204: 6.532