Starting phenix.real_space_refine on Sun Mar 24 06:35:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fep_31559/03_2024/7fep_31559_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fep_31559/03_2024/7fep_31559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fep_31559/03_2024/7fep_31559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fep_31559/03_2024/7fep_31559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fep_31559/03_2024/7fep_31559_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fep_31559/03_2024/7fep_31559_updated.pdb" } resolution = 3.1 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= 0.006 sd= 0.269 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: 5 Type Number sf(0) Gaussians S 98 5.16 5 C 13356 2.51 5 N 3528 2.21 5 O 4046 1.98 5 H 19353 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ASP 36": "OD1" <-> "OD2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ASP 36": "OD1" <-> "OD2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ASP 36": "OD1" <-> "OD2" Residue "F TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "G ARG 12": "NH1" <-> "NH2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "I ARG 12": "NH1" <-> "NH2" Residue "I ASP 36": "OD1" <-> "OD2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "J ARG 12": "NH1" <-> "NH2" Residue "J ASP 36": "OD1" <-> "OD2" Residue "J TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "K ARG 12": "NH1" <-> "NH2" Residue "K ASP 36": "OD1" <-> "OD2" Residue "K TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "L ARG 12": "NH1" <-> "NH2" Residue "L ASP 36": "OD1" <-> "OD2" Residue "L TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 134": "OE1" <-> "OE2" Residue "M ARG 12": "NH1" <-> "NH2" Residue "M ASP 36": "OD1" <-> "OD2" Residue "M TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 134": "OE1" <-> "OE2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ASP 36": "OD1" <-> "OD2" Residue "N TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 134": "OE1" <-> "OE2" Residue "H ARG 12": "NH1" <-> "NH2" Residue "H ASP 36": "OD1" <-> "OD2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 134": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40381 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2815 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "B" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2840 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "C" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2821 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "D" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2840 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "E" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2849 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "F" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2840 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "G" Number of atoms: 2831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2831 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "I" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2840 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "J" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2840 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "K" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2840 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "L" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2822 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "M" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2822 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "N" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2827 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "H" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2826 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "O" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT O 1 " pdbres="PHE O 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT P 1 " pdbres="PHE P 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Q 1 " pdbres="PHE Q 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT R 1 " pdbres="PHE R 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT S 1 " pdbres="PHE S 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT T 1 " pdbres="PHE T 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT U 1 " pdbres="PHE U 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT V 1 " pdbres="PHE V 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT W 1 " pdbres="PHE W 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT X 1 " pdbres="PHE X 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Y 1 " pdbres="PHE Y 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Z 1 " pdbres="PHE Z 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "a" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT a 1 " pdbres="PHE a 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "b" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT b 1 " pdbres="PHE b 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 17.27, per 1000 atoms: 0.43 Number of scatterers: 40381 At special positions: 0 Unit cell: (122.08, 118.72, 128.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 O 4046 8.00 N 3528 7.00 C 13356 6.00 H 19353 1.00 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=28, symmetry=0 Number of additional bonds: simple=28, symmetry=0 Coordination: Other bonds: Time building additional restraints: 28.53 Conformation dependent library (CDL) restraints added in 4.1 seconds 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 36 sheets defined 40.1% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.77 Creating SS restraints... Processing helix chain 'A' and resid 19 through 26 removed outlier: 3.823A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 26' Processing helix chain 'A' and resid 37 through 53 removed outlier: 3.512A pdb=" N ASN A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.792A pdb=" N THR A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 81 " --> pdb=" O TYR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 105 removed outlier: 3.539A pdb=" N ALA A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.725A pdb=" N GLU A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 167 No H-bonds generated for 'chain 'A' and resid 164 through 167' Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'B' and resid 19 through 26 removed outlier: 3.823A pdb=" N LEU B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 25 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 26' Processing helix chain 'B' and resid 37 through 53 removed outlier: 3.514A pdb=" N ASN B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.793A pdb=" N THR B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 105 removed outlier: 3.539A pdb=" N ALA B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 157 removed outlier: 3.725A pdb=" N GLU B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 removed outlier: 3.704A pdb=" N ARG B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'C' and resid 19 through 26 removed outlier: 3.824A pdb=" N LEU C 23 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS C 25 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 19 through 26' Processing helix chain 'C' and resid 37 through 53 removed outlier: 3.513A pdb=" N ASN C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 48 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 82 removed outlier: 3.793A pdb=" N THR C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN C 81 " --> pdb=" O TYR C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 105 removed outlier: 3.540A pdb=" N ALA C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C 105 " --> pdb=" O PHE C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 157 removed outlier: 3.725A pdb=" N GLU C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE C 137 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 167 removed outlier: 3.705A pdb=" N ARG C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'D' and resid 19 through 26 removed outlier: 3.824A pdb=" N LEU D 23 " --> pdb=" O ILE D 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 25 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 19 through 26' Processing helix chain 'D' and resid 37 through 53 removed outlier: 3.513A pdb=" N ASN D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER D 42 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU D 53 " --> pdb=" O PHE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 82 removed outlier: 3.793A pdb=" N THR D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN D 81 " --> pdb=" O TYR D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 105 removed outlier: 3.540A pdb=" N ALA D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 105 " --> pdb=" O PHE D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 157 removed outlier: 3.725A pdb=" N GLU D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE D 137 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU D 143 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU D 155 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 167 removed outlier: 3.705A pdb=" N ARG D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'E' and resid 19 through 26 removed outlier: 3.823A pdb=" N LEU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS E 25 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 19 through 26' Processing helix chain 'E' and resid 37 through 53 removed outlier: 3.513A pdb=" N ASN E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER E 42 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU E 48 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 82 removed outlier: 3.793A pdb=" N THR E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN E 81 " --> pdb=" O TYR E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 105 removed outlier: 3.539A pdb=" N ALA E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA E 105 " --> pdb=" O PHE E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 157 removed outlier: 3.725A pdb=" N GLU E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE E 137 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU E 143 " --> pdb=" O ALA E 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA E 154 " --> pdb=" O ASN E 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 167 removed outlier: 3.704A pdb=" N ARG E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'F' and resid 19 through 26 removed outlier: 3.823A pdb=" N LEU F 23 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU F 24 " --> pdb=" O TYR F 20 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F 25 " --> pdb=" O SER F 21 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 19 through 26' Processing helix chain 'F' and resid 37 through 53 removed outlier: 3.513A pdb=" N ASN F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER F 42 " --> pdb=" O ASN F 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER F 45 " --> pdb=" O ASN F 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU F 48 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU F 53 " --> pdb=" O PHE F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 82 removed outlier: 3.793A pdb=" N THR F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN F 81 " --> pdb=" O TYR F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 105 removed outlier: 3.540A pdb=" N ALA F 104 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA F 105 " --> pdb=" O PHE F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 157 removed outlier: 3.724A pdb=" N GLU F 136 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE F 137 " --> pdb=" O THR F 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS F 140 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU F 143 " --> pdb=" O ALA F 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA F 154 " --> pdb=" O ASN F 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 182 No H-bonds generated for 'chain 'F' and resid 179 through 182' Processing helix chain 'G' and resid 19 through 26 removed outlier: 3.824A pdb=" N LEU G 23 " --> pdb=" O ILE G 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU G 24 " --> pdb=" O TYR G 20 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS G 25 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 19 through 26' Processing helix chain 'G' and resid 37 through 53 removed outlier: 3.514A pdb=" N ASN G 41 " --> pdb=" O ASP G 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER G 42 " --> pdb=" O ASN G 38 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU G 48 " --> pdb=" O VAL G 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU G 53 " --> pdb=" O PHE G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 82 removed outlier: 3.792A pdb=" N THR G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN G 81 " --> pdb=" O TYR G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 105 removed outlier: 3.539A pdb=" N ALA G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA G 105 " --> pdb=" O PHE G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 157 removed outlier: 3.724A pdb=" N GLU G 136 " --> pdb=" O ALA G 132 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE G 137 " --> pdb=" O THR G 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS G 140 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU G 143 " --> pdb=" O ALA G 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA G 154 " --> pdb=" O ASN G 150 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 182 Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.824A pdb=" N LEU I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS I 25 " --> pdb=" O SER I 21 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 19 through 26' Processing helix chain 'I' and resid 37 through 53 removed outlier: 3.514A pdb=" N ASN I 41 " --> pdb=" O ASP I 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER I 42 " --> pdb=" O ASN I 38 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER I 45 " --> pdb=" O ASN I 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU I 48 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA I 52 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU I 53 " --> pdb=" O PHE I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 82 removed outlier: 3.793A pdb=" N THR I 79 " --> pdb=" O ALA I 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN I 81 " --> pdb=" O TYR I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 105 removed outlier: 3.539A pdb=" N ALA I 104 " --> pdb=" O ALA I 100 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA I 105 " --> pdb=" O PHE I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 157 removed outlier: 3.725A pdb=" N GLU I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE I 137 " --> pdb=" O THR I 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA I 138 " --> pdb=" O GLU I 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS I 140 " --> pdb=" O GLU I 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU I 143 " --> pdb=" O ALA I 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU I 144 " --> pdb=" O LYS I 140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN I 150 " --> pdb=" O ARG I 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS I 151 " --> pdb=" O ASP I 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL I 152 " --> pdb=" O LYS I 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA I 154 " --> pdb=" O ASN I 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU I 155 " --> pdb=" O LYS I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 167 removed outlier: 3.705A pdb=" N ARG I 166 " --> pdb=" O GLU I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 182 Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.823A pdb=" N LEU J 23 " --> pdb=" O ILE J 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU J 24 " --> pdb=" O TYR J 20 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS J 25 " --> pdb=" O SER J 21 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 19 through 26' Processing helix chain 'J' and resid 37 through 53 removed outlier: 3.513A pdb=" N ASN J 41 " --> pdb=" O ASP J 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER J 42 " --> pdb=" O ASN J 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER J 45 " --> pdb=" O ASN J 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU J 48 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA J 52 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU J 53 " --> pdb=" O PHE J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 82 removed outlier: 3.793A pdb=" N THR J 79 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN J 81 " --> pdb=" O TYR J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 103 Processing helix chain 'J' and resid 132 through 157 removed outlier: 3.725A pdb=" N GLU J 136 " --> pdb=" O ALA J 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE J 137 " --> pdb=" O THR J 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS J 140 " --> pdb=" O GLU J 136 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU J 143 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU J 144 " --> pdb=" O LYS J 140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN J 150 " --> pdb=" O ARG J 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS J 151 " --> pdb=" O ASP J 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL J 152 " --> pdb=" O LYS J 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA J 154 " --> pdb=" O ASN J 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU J 155 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 167 removed outlier: 3.705A pdb=" N ARG J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 182 Processing helix chain 'K' and resid 19 through 23 removed outlier: 3.823A pdb=" N LEU K 23 " --> pdb=" O ILE K 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 19 through 23' Processing helix chain 'K' and resid 37 through 48 removed outlier: 3.513A pdb=" N ASN K 41 " --> pdb=" O ASP K 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER K 42 " --> pdb=" O ASN K 38 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER K 45 " --> pdb=" O ASN K 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU K 48 " --> pdb=" O VAL K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 82 removed outlier: 3.792A pdb=" N THR K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN K 81 " --> pdb=" O TYR K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 103 Processing helix chain 'K' and resid 132 through 153 removed outlier: 3.725A pdb=" N GLU K 136 " --> pdb=" O ALA K 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE K 137 " --> pdb=" O THR K 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA K 138 " --> pdb=" O GLU K 134 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS K 140 " --> pdb=" O GLU K 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU K 143 " --> pdb=" O ALA K 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU K 144 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN K 150 " --> pdb=" O ARG K 146 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS K 151 " --> pdb=" O ASP K 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL K 152 " --> pdb=" O LYS K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 167 removed outlier: 3.705A pdb=" N ARG K 166 " --> pdb=" O GLU K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 182 No H-bonds generated for 'chain 'K' and resid 179 through 182' Processing helix chain 'L' and resid 19 through 23 removed outlier: 3.823A pdb=" N LEU L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 19 through 23' Processing helix chain 'L' and resid 37 through 53 removed outlier: 3.513A pdb=" N ASN L 41 " --> pdb=" O ASP L 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER L 42 " --> pdb=" O ASN L 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER L 45 " --> pdb=" O ASN L 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU L 48 " --> pdb=" O VAL L 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA L 52 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU L 53 " --> pdb=" O PHE L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 82 removed outlier: 3.792A pdb=" N THR L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN L 81 " --> pdb=" O TYR L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 103 No H-bonds generated for 'chain 'L' and resid 100 through 103' Processing helix chain 'L' and resid 132 through 157 removed outlier: 3.725A pdb=" N GLU L 136 " --> pdb=" O ALA L 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE L 137 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA L 138 " --> pdb=" O GLU L 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS L 140 " --> pdb=" O GLU L 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU L 143 " --> pdb=" O ALA L 139 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU L 144 " --> pdb=" O LYS L 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS L 151 " --> pdb=" O ASP L 147 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL L 152 " --> pdb=" O LYS L 148 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA L 154 " --> pdb=" O ASN L 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU L 155 " --> pdb=" O LYS L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 167 removed outlier: 3.704A pdb=" N ARG L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 182 No H-bonds generated for 'chain 'L' and resid 179 through 182' Processing helix chain 'M' and resid 19 through 26 removed outlier: 3.823A pdb=" N LEU M 23 " --> pdb=" O ILE M 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU M 24 " --> pdb=" O TYR M 20 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS M 25 " --> pdb=" O SER M 21 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 19 through 26' Processing helix chain 'M' and resid 37 through 50 removed outlier: 3.513A pdb=" N ASN M 41 " --> pdb=" O ASP M 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER M 42 " --> pdb=" O ASN M 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER M 45 " --> pdb=" O ASN M 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU M 48 " --> pdb=" O VAL M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 82 removed outlier: 3.793A pdb=" N THR M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN M 81 " --> pdb=" O TYR M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 105 removed outlier: 3.540A pdb=" N ALA M 104 " --> pdb=" O ALA M 100 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA M 105 " --> pdb=" O PHE M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 157 removed outlier: 3.725A pdb=" N GLU M 136 " --> pdb=" O ALA M 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE M 137 " --> pdb=" O THR M 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA M 138 " --> pdb=" O GLU M 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS M 140 " --> pdb=" O GLU M 136 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU M 143 " --> pdb=" O ALA M 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU M 144 " --> pdb=" O LYS M 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN M 150 " --> pdb=" O ARG M 146 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS M 151 " --> pdb=" O ASP M 147 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL M 152 " --> pdb=" O LYS M 148 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA M 154 " --> pdb=" O ASN M 150 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU M 155 " --> pdb=" O LYS M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 167 No H-bonds generated for 'chain 'M' and resid 164 through 167' Processing helix chain 'M' and resid 178 through 182 Processing helix chain 'N' and resid 19 through 23 removed outlier: 3.824A pdb=" N LEU N 23 " --> pdb=" O ILE N 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 19 through 23' Processing helix chain 'N' and resid 37 through 53 removed outlier: 3.513A pdb=" N ASN N 41 " --> pdb=" O ASP N 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER N 42 " --> pdb=" O ASN N 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER N 45 " --> pdb=" O ASN N 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU N 53 " --> pdb=" O PHE N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 82 removed outlier: 3.792A pdb=" N THR N 79 " --> pdb=" O ALA N 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN N 81 " --> pdb=" O TYR N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 105 removed outlier: 3.540A pdb=" N ALA N 104 " --> pdb=" O ALA N 100 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA N 105 " --> pdb=" O PHE N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 157 removed outlier: 3.725A pdb=" N GLU N 136 " --> pdb=" O ALA N 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE N 137 " --> pdb=" O THR N 133 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA N 138 " --> pdb=" O GLU N 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS N 140 " --> pdb=" O GLU N 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU N 143 " --> pdb=" O ALA N 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU N 144 " --> pdb=" O LYS N 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN N 150 " --> pdb=" O ARG N 146 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS N 151 " --> pdb=" O ASP N 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL N 152 " --> pdb=" O LYS N 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA N 154 " --> pdb=" O ASN N 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU N 155 " --> pdb=" O LYS N 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 167 removed outlier: 3.705A pdb=" N ARG N 166 " --> pdb=" O GLU N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 182 Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.823A pdb=" N LEU H 23 " --> pdb=" O ILE H 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 19 through 26' Processing helix chain 'H' and resid 37 through 53 removed outlier: 3.514A pdb=" N ASN H 41 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER H 42 " --> pdb=" O ASN H 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER H 45 " --> pdb=" O ASN H 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA H 52 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU H 53 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 82 removed outlier: 3.792A pdb=" N THR H 79 " --> pdb=" O ALA H 75 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN H 81 " --> pdb=" O TYR H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 105 removed outlier: 3.539A pdb=" N ALA H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA H 105 " --> pdb=" O PHE H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 157 removed outlier: 3.724A pdb=" N GLU H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE H 137 " --> pdb=" O THR H 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA H 138 " --> pdb=" O GLU H 134 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS H 140 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU H 143 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU H 144 " --> pdb=" O LYS H 140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS H 151 " --> pdb=" O ASP H 147 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL H 152 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA H 154 " --> pdb=" O ASN H 150 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU H 155 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 167 removed outlier: 3.705A pdb=" N ARG H 166 " --> pdb=" O GLU H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 181 No H-bonds generated for 'chain 'H' and resid 178 through 181' Processing sheet with id= A, first strand: chain 'A' and resid 5 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.554A pdb=" N CYS A 91 " --> pdb=" O TYR A 112 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.568A pdb=" N ILE A 121 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 172 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 5 through 8 Processing sheet with id= E, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.554A pdb=" N CYS B 91 " --> pdb=" O TYR B 112 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 119 through 121 removed outlier: 3.569A pdb=" N ILE B 121 " --> pdb=" O ASN B 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 172 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 5 through 8 Processing sheet with id= H, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.554A pdb=" N CYS C 91 " --> pdb=" O TYR C 112 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 119 through 121 removed outlier: 3.570A pdb=" N ILE C 121 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 172 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 5 through 8 Processing sheet with id= K, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.554A pdb=" N CYS D 91 " --> pdb=" O TYR D 112 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 119 through 121 removed outlier: 3.569A pdb=" N ILE D 121 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN D 172 " --> pdb=" O ILE D 121 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 5 through 8 Processing sheet with id= N, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.554A pdb=" N CYS E 91 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 119 through 121 removed outlier: 3.569A pdb=" N ILE E 121 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN E 172 " --> pdb=" O ILE E 121 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 5 through 8 Processing sheet with id= Q, first strand: chain 'G' and resid 5 through 8 Processing sheet with id= R, first strand: chain 'G' and resid 89 through 91 removed outlier: 3.554A pdb=" N CYS G 91 " --> pdb=" O TYR G 112 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 5 through 8 Processing sheet with id= T, first strand: chain 'I' and resid 89 through 91 removed outlier: 3.555A pdb=" N CYS I 91 " --> pdb=" O TYR I 112 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 119 through 121 removed outlier: 3.570A pdb=" N ILE I 121 " --> pdb=" O ASN I 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN I 172 " --> pdb=" O ILE I 121 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 5 through 8 Processing sheet with id= W, first strand: chain 'K' and resid 6 through 8 Processing sheet with id= X, first strand: chain 'K' and resid 89 through 91 removed outlier: 3.554A pdb=" N CYS K 91 " --> pdb=" O TYR K 112 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= Z, first strand: chain 'L' and resid 89 through 91 removed outlier: 3.554A pdb=" N CYS L 91 " --> pdb=" O TYR L 112 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 119 through 121 removed outlier: 3.570A pdb=" N ILE L 121 " --> pdb=" O ASN L 172 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN L 172 " --> pdb=" O ILE L 121 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'M' and resid 5 through 8 Processing sheet with id= AC, first strand: chain 'M' and resid 89 through 91 removed outlier: 3.554A pdb=" N CYS M 91 " --> pdb=" O TYR M 112 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 119 through 121 removed outlier: 3.569A pdb=" N ILE M 121 " --> pdb=" O ASN M 172 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN M 172 " --> pdb=" O ILE M 121 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 5 through 8 Processing sheet with id= AF, first strand: chain 'N' and resid 89 through 91 removed outlier: 3.553A pdb=" N CYS N 91 " --> pdb=" O TYR N 112 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 119 through 121 removed outlier: 3.569A pdb=" N ILE N 121 " --> pdb=" O ASN N 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN N 172 " --> pdb=" O ILE N 121 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 5 through 8 Processing sheet with id= AI, first strand: chain 'H' and resid 89 through 91 removed outlier: 3.554A pdb=" N CYS H 91 " --> pdb=" O TYR H 112 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 119 through 121 removed outlier: 3.569A pdb=" N ILE H 121 " --> pdb=" O ASN H 172 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN H 172 " --> pdb=" O ILE H 121 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1308 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: 13.39 Time building geometry restraints manager: 29.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 19328 1.00 - 1.20: 25 1.20 - 1.40: 7966 1.40 - 1.60: 13104 1.60 - 1.80: 210 Bond restraints: 40633 Sorted by residual: bond pdb=" C ALA W 6 " pdb=" N MP8 W 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.76e+01 bond pdb=" C ALA T 6 " pdb=" N MP8 T 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.72e+01 bond pdb=" C ALA X 6 " pdb=" N MP8 X 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.68e+01 bond pdb=" C ALA Y 6 " pdb=" N MP8 Y 7 " ideal model delta sigma weight residual 1.329 1.466 -0.137 1.40e-02 5.10e+03 9.64e+01 bond pdb=" C ALA O 6 " pdb=" N MP8 O 7 " ideal model delta sigma weight residual 1.329 1.466 -0.137 1.40e-02 5.10e+03 9.63e+01 ... (remaining 40628 not shown) Histogram of bond angle deviations from ideal: 51.11 - 69.52: 382 69.52 - 87.93: 961 87.93 - 106.34: 1762 106.34 - 124.76: 68553 124.76 - 143.17: 1165 Bond angle restraints: 72823 Sorted by residual: angle pdb=" CA GLY E 13 " pdb=" N GLY E 13 " pdb=" H GLY E 13 " ideal model delta sigma weight residual 113.82 51.11 62.71 3.00e+00 1.11e-01 4.37e+02 angle pdb=" C THR G 168 " pdb=" N ASP G 169 " pdb=" H ASP G 169 " ideal model delta sigma weight residual 124.38 61.68 62.70 3.00e+00 1.11e-01 4.37e+02 angle pdb=" CA ILE K 43 " pdb=" N ILE K 43 " pdb=" H ILE K 43 " ideal model delta sigma weight residual 114.62 53.77 60.85 3.00e+00 1.11e-01 4.11e+02 angle pdb=" CA LEU G 144 " pdb=" N LEU G 144 " pdb=" H LEU G 144 " ideal model delta sigma weight residual 114.71 53.97 60.74 3.00e+00 1.11e-01 4.10e+02 angle pdb=" CA GLU E 14 " pdb=" N GLU E 14 " pdb=" H GLU E 14 " ideal model delta sigma weight residual 113.46 53.05 60.41 3.00e+00 1.11e-01 4.05e+02 ... (remaining 72818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 16167 15.54 - 31.09: 1985 31.09 - 46.63: 615 46.63 - 62.17: 356 62.17 - 77.72: 2 Dihedral angle restraints: 19125 sinusoidal: 10617 harmonic: 8508 Sorted by residual: dihedral pdb=" CA ASP B 169 " pdb=" C ASP B 169 " pdb=" N ARG B 170 " pdb=" CA ARG B 170 " ideal model delta harmonic sigma weight residual -180.00 -153.19 -26.81 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ASP A 169 " pdb=" C ASP A 169 " pdb=" N ARG A 170 " pdb=" CA ARG A 170 " ideal model delta harmonic sigma weight residual -180.00 -153.19 -26.81 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ASP L 169 " pdb=" C ASP L 169 " pdb=" N ARG L 170 " pdb=" CA ARG L 170 " ideal model delta harmonic sigma weight residual -180.00 -153.20 -26.80 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 19122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2148 0.084 - 0.169: 858 0.169 - 0.253: 201 0.253 - 0.338: 111 0.338 - 0.422: 42 Chirality restraints: 3360 Sorted by residual: chirality pdb=" CG LEU B 144 " pdb=" CB LEU B 144 " pdb=" CD1 LEU B 144 " pdb=" CD2 LEU B 144 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CG LEU M 144 " pdb=" CB LEU M 144 " pdb=" CD1 LEU M 144 " pdb=" CD2 LEU M 144 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CG LEU E 144 " pdb=" CB LEU E 144 " pdb=" CD1 LEU E 144 " pdb=" CD2 LEU E 144 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.41e+00 ... (remaining 3357 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 13 " 0.022 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" N GLU E 14 " -0.009 2.00e-02 2.50e+03 pdb=" CA GLU E 14 " 0.024 2.00e-02 2.50e+03 pdb=" H GLU E 14 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 168 " -0.020 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" N ASP F 169 " 0.011 2.00e-02 2.50e+03 pdb=" CA ASP F 169 " -0.020 2.00e-02 2.50e+03 pdb=" H ASP F 169 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G 168 " 0.019 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" N ASP G 169 " -0.008 2.00e-02 2.50e+03 pdb=" CA ASP G 169 " 0.017 2.00e-02 2.50e+03 pdb=" H ASP G 169 " -0.028 2.00e-02 2.50e+03 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.01: 1498 2.01 - 2.66: 53093 2.66 - 3.31: 99524 3.31 - 3.95: 129251 3.95 - 4.60: 210895 Nonbonded interactions: 494261 Sorted by model distance: nonbonded pdb=" H ASP G 169 " pdb=" HA ASP G 169 " model vdw 1.367 1.816 nonbonded pdb=" H LEU J 61 " pdb=" HA LEU J 61 " model vdw 1.456 1.816 nonbonded pdb=" H ILE K 188 " pdb=" HA ILE K 188 " model vdw 1.457 1.816 nonbonded pdb=" H MET F 120 " pdb=" HA MET F 120 " model vdw 1.460 1.816 nonbonded pdb=" H LEU K 61 " pdb=" HA LEU K 61 " model vdw 1.461 1.816 ... (remaining 494256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name C \ Z or name OH )) or resid 18 or (resid 19 and (name N or name CA or name C or nam \ e O or name CB or name CG1 or name CG2 or name CD1 or name HA )) or resid 20 thr \ ough 58 or (resid 59 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1 or name H or name HA )) or resid 60 through 190)) \ selection = (chain 'B' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 or (resid 19 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 or (resid 48 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 49 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ \ )) or resid 50 through 58 or (resid 59 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 60 through 190)) selection = (chain 'C' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 through 47 or (resid 48 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2)) or (resid 49 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or nam \ e CE2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or n \ ame HE1 or name HE2 or name HZ )) or resid 50 through 190)) selection = (chain 'D' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 or (resid 19 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 or (resid 48 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 49 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ \ )) or resid 50 through 58 or (resid 59 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 60 through 190)) selection = (chain 'E' and (resid 2 through 12 or (resid 13 and (name N or name CA or name C \ or name O )) or (resid 14 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2)) or (resid 15 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1 or name NH2)) or (resid 16 and (name N or name CA or name C or name \ O or name CB )) or (resid 17 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name \ OH )) or resid 18 or (resid 19 and (name N or name CA or name C or name O or na \ me CB or name CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 o \ r (resid 48 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2)) or (resid 49 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name H \ E2 or name HZ )) or resid 50 through 58 or (resid 59 and (name N or name CA or n \ ame C or name O or name CB or name CG1 or name CG2 or name CD1 or name H or name \ HA )) or resid 60 through 190)) selection = (chain 'F' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 or (resid 19 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 or (resid 48 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 49 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ \ )) or resid 50 through 58 or (resid 59 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 60 through 190)) selection = (chain 'G' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or resid 17 through 18 or (resid 19 and (name N or name CA or name C or name O \ or name CB or name CG1 or name CG2 or name CD1 or name HA )) or resid 20 throug \ h 47 or (resid 48 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2)) or (resid 49 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or na \ me CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or \ name HE2 or name HZ )) or resid 50 through 58 or (resid 59 and (name N or name C \ A or name C or name O or name CB or name CG1 or name CG2 or name CD1 or name H o \ r name HA )) or resid 60 through 190)) selection = (chain 'H' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 or (resid 19 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 or (resid 48 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 49 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ \ )) or resid 50 through 58 or (resid 59 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 60 through 190)) selection = (chain 'I' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 or (resid 19 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 or (resid 48 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 49 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ \ )) or resid 50 through 58 or (resid 59 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 60 through 190)) selection = (chain 'J' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 or (resid 19 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 or (resid 48 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 49 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ \ )) or resid 50 through 58 or (resid 59 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 60 through 190)) selection = (chain 'K' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 or (resid 19 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 or (resid 48 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 49 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ \ )) or resid 50 through 58 or (resid 59 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 60 through 190)) selection = (chain 'L' and (resid 2 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH )) or resid 18 or (resid 19 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2 or name CD1 or name HA )) or re \ sid 20 through 47 or (resid 48 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD1 or name CD2)) or (resid 49 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or n \ ame CE2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or \ name HE1 or name HE2 or name HZ )) or resid 50 through 58 or (resid 59 and (nam \ e N or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD \ 1 or name H or name HA )) or resid 60 through 190)) selection = (chain 'M' and (resid 2 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH )) or resid 18 or (resid 19 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2 or name CD1 or name HA )) or re \ sid 20 through 47 or (resid 48 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD1 or name CD2)) or (resid 49 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or n \ ame CE2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or \ name HE1 or name HE2 or name HZ )) or resid 50 through 58 or (resid 59 and (nam \ e N or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD \ 1 or name H or name HA )) or resid 60 through 190)) selection = (chain 'N' and (resid 2 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name C \ Z or name OH )) or resid 18 or (resid 19 and (name N or name CA or name C or nam \ e O or name CB or name CG1 or name CG2 or name CD1 or name HA )) or resid 20 thr \ ough 47 or (resid 48 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD1 or name CD2)) or (resid 49 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or \ name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 \ or name HE2 or name HZ )) or resid 50 through 58 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB or name CG1 or name CG2 or name CD1 or name \ H or name HA )) or resid 60 through 190)) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } 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: 0.520 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: 0.610 Extract box with map and model: 4.790 Check model and map are aligned: 0.560 Set scattering table: 0.370 Process input model: 117.170 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.320 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 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 : 0.015 0.138 21280 Z= 0.957 Angle : 1.256 9.103 28658 Z= 0.661 Chirality : 0.110 0.422 3360 Planarity : 0.005 0.037 3724 Dihedral : 14.371 61.454 8092 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.57 % Favored : 89.89 % Rotamer: Outliers : 2.53 % Allowed : 1.90 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.30 (0.11), residues: 2632 helix: -3.60 (0.10), residues: 1106 sheet: -3.00 (0.20), residues: 434 loop : -3.47 (0.13), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS F 122 PHE 0.006 0.001 PHE A 49 TYR 0.020 0.002 TYR M 17 ARG 0.006 0.001 ARG M 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 612 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 556 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.6959 (ttmm) cc_final: 0.6641 (tttt) REVERT: A 108 LYS cc_start: 0.8325 (tptm) cc_final: 0.7795 (tppt) REVERT: A 169 ASP cc_start: 0.7652 (t70) cc_final: 0.7349 (t0) REVERT: A 181 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7354 (mt-10) REVERT: A 186 ASP cc_start: 0.7979 (m-30) cc_final: 0.7675 (m-30) REVERT: B 8 GLU cc_start: 0.6630 (tm-30) cc_final: 0.6172 (tt0) REVERT: B 84 LYS cc_start: 0.7131 (ttmm) cc_final: 0.6820 (tttt) REVERT: B 108 LYS cc_start: 0.8606 (tptm) cc_final: 0.8254 (tppt) REVERT: B 118 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6812 (mm-30) REVERT: C 84 LYS cc_start: 0.7426 (ttmm) cc_final: 0.7188 (mtpt) REVERT: C 89 THR cc_start: 0.7688 (p) cc_final: 0.7415 (p) REVERT: C 108 LYS cc_start: 0.8453 (tptm) cc_final: 0.7991 (tppt) REVERT: C 118 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7042 (mm-30) REVERT: C 151 LYS cc_start: 0.7542 (tppp) cc_final: 0.7317 (mttt) REVERT: C 165 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7473 (mt-10) REVERT: D 84 LYS cc_start: 0.7248 (ttmm) cc_final: 0.6939 (tttt) REVERT: D 107 GLU cc_start: 0.5819 (tp30) cc_final: 0.5591 (tp30) REVERT: D 108 LYS cc_start: 0.8328 (tptm) cc_final: 0.7566 (tppt) REVERT: E 84 LYS cc_start: 0.6818 (ttmm) cc_final: 0.6571 (tttt) REVERT: E 108 LYS cc_start: 0.8262 (tptm) cc_final: 0.7716 (tppt) REVERT: E 116 ASN cc_start: 0.6863 (p0) cc_final: 0.5524 (p0) REVERT: F 8 GLU cc_start: 0.6820 (tm-30) cc_final: 0.6493 (tt0) REVERT: F 84 LYS cc_start: 0.7105 (ttmm) cc_final: 0.6762 (tttt) REVERT: F 108 LYS cc_start: 0.8314 (tptm) cc_final: 0.7744 (tppt) REVERT: F 156 ARG cc_start: 0.6337 (mmt180) cc_final: 0.6080 (mmt180) REVERT: F 186 ASP cc_start: 0.7670 (m-30) cc_final: 0.7161 (m-30) REVERT: G 8 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6315 (tt0) REVERT: G 37 ASP cc_start: 0.6567 (OUTLIER) cc_final: 0.6203 (m-30) REVERT: G 118 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6989 (mm-30) REVERT: I 84 LYS cc_start: 0.7254 (ttmm) cc_final: 0.6977 (tttt) REVERT: I 108 LYS cc_start: 0.8428 (tptm) cc_final: 0.7822 (tppt) REVERT: I 186 ASP cc_start: 0.7645 (m-30) cc_final: 0.7223 (m-30) REVERT: J 6 VAL cc_start: 0.7195 (OUTLIER) cc_final: 0.6923 (m) REVERT: J 108 LYS cc_start: 0.8344 (tptm) cc_final: 0.7912 (tppt) REVERT: J 110 LYS cc_start: 0.6017 (mttp) cc_final: 0.5762 (mtmm) REVERT: J 129 GLN cc_start: 0.8533 (tt0) cc_final: 0.8276 (tt0) REVERT: K 8 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6612 (tt0) REVERT: K 84 LYS cc_start: 0.7139 (ttmm) cc_final: 0.6852 (ttpt) REVERT: K 108 LYS cc_start: 0.8359 (tptm) cc_final: 0.7889 (tppt) REVERT: K 116 ASN cc_start: 0.6908 (p0) cc_final: 0.5689 (p0) REVERT: K 172 ASN cc_start: 0.6632 (t0) cc_final: 0.6380 (t0) REVERT: K 186 ASP cc_start: 0.8165 (m-30) cc_final: 0.7756 (m-30) REVERT: L 8 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6918 (tt0) REVERT: L 84 LYS cc_start: 0.7369 (ttmm) cc_final: 0.7166 (tttt) REVERT: L 108 LYS cc_start: 0.8544 (tptm) cc_final: 0.7932 (tppt) REVERT: M 8 GLU cc_start: 0.6602 (tm-30) cc_final: 0.6263 (tt0) REVERT: M 54 ASP cc_start: 0.6730 (t0) cc_final: 0.6301 (t0) REVERT: M 58 GLU cc_start: 0.6987 (tt0) cc_final: 0.6690 (tt0) REVERT: M 84 LYS cc_start: 0.7092 (ttmm) cc_final: 0.6770 (tttt) REVERT: N 108 LYS cc_start: 0.8533 (tptm) cc_final: 0.8167 (tppt) REVERT: N 165 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7795 (mt-10) REVERT: H 84 LYS cc_start: 0.7450 (ttmm) cc_final: 0.7223 (mtpt) REVERT: H 89 THR cc_start: 0.7646 (p) cc_final: 0.7379 (p) REVERT: H 108 LYS cc_start: 0.8340 (tptm) cc_final: 0.7955 (tppt) REVERT: H 165 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7233 (mt-10) outliers start: 56 outliers final: 4 residues processed: 598 average time/residue: 0.7597 time to fit residues: 665.9001 Evaluate side-chains 392 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 386 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain M residue 2 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 228 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21280 Z= 0.207 Angle : 1.408 23.665 28658 Z= 0.760 Chirality : 0.248 1.666 3360 Planarity : 0.004 0.040 3724 Dihedral : 5.469 33.688 2993 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.67 % Favored : 91.79 % Rotamer: Outliers : 1.67 % Allowed : 8.68 % Favored : 89.65 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.13), residues: 2632 helix: -2.59 (0.13), residues: 1106 sheet: -2.60 (0.22), residues: 434 loop : -2.79 (0.15), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS J 122 PHE 0.006 0.001 PHE I 49 TYR 0.014 0.001 TYR K 17 ARG 0.003 0.000 ARG E 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 445 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 408 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8273 (tptm) cc_final: 0.7797 (tppt) REVERT: B 108 LYS cc_start: 0.8290 (tptm) cc_final: 0.7584 (tppt) REVERT: B 118 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6900 (mm-30) REVERT: C 89 THR cc_start: 0.7660 (p) cc_final: 0.7386 (p) REVERT: C 108 LYS cc_start: 0.8394 (tptm) cc_final: 0.7880 (tppt) REVERT: C 118 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7094 (mm-30) REVERT: C 151 LYS cc_start: 0.7486 (tppp) cc_final: 0.7254 (mttt) REVERT: D 108 LYS cc_start: 0.8268 (tptm) cc_final: 0.7721 (tppt) REVERT: D 186 ASP cc_start: 0.8055 (m-30) cc_final: 0.7689 (m-30) REVERT: E 108 LYS cc_start: 0.8323 (tptm) cc_final: 0.7874 (tppt) REVERT: F 84 LYS cc_start: 0.6998 (ttmm) cc_final: 0.6677 (tttt) REVERT: F 108 LYS cc_start: 0.8146 (tptm) cc_final: 0.7640 (tppt) REVERT: F 186 ASP cc_start: 0.7826 (m-30) cc_final: 0.7373 (m-30) REVERT: G 151 LYS cc_start: 0.7234 (mtpp) cc_final: 0.6790 (mttt) REVERT: I 84 LYS cc_start: 0.7587 (ttmm) cc_final: 0.7284 (tttt) REVERT: I 89 THR cc_start: 0.7354 (p) cc_final: 0.7098 (p) REVERT: I 108 LYS cc_start: 0.8266 (tptm) cc_final: 0.7601 (tppt) REVERT: I 186 ASP cc_start: 0.7695 (m-30) cc_final: 0.7193 (m-30) REVERT: J 84 LYS cc_start: 0.6914 (ttmm) cc_final: 0.6619 (tttt) REVERT: J 108 LYS cc_start: 0.8310 (tptm) cc_final: 0.7890 (tppt) REVERT: J 110 LYS cc_start: 0.6053 (mttp) cc_final: 0.5786 (mtmm) REVERT: J 120 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.7004 (ttm) REVERT: K 108 LYS cc_start: 0.8449 (tptm) cc_final: 0.7873 (tppt) REVERT: L 108 LYS cc_start: 0.8495 (tptm) cc_final: 0.8033 (tppt) REVERT: L 116 ASN cc_start: 0.6411 (OUTLIER) cc_final: 0.5792 (p0) REVERT: M 33 SER cc_start: 0.8321 (t) cc_final: 0.8067 (t) REVERT: N 108 LYS cc_start: 0.8317 (tptm) cc_final: 0.7759 (tppt) REVERT: H 89 THR cc_start: 0.7630 (p) cc_final: 0.7367 (p) REVERT: H 108 LYS cc_start: 0.8263 (tptm) cc_final: 0.7816 (tppt) REVERT: H 165 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6941 (mt-10) outliers start: 37 outliers final: 15 residues processed: 418 average time/residue: 0.8513 time to fit residues: 520.6182 Evaluate side-chains 397 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 380 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain K residue 166 ARG Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain H residue 166 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 0.0970 chunk 227 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21280 Z= 0.228 Angle : 1.396 22.910 28658 Z= 0.751 Chirality : 0.249 1.694 3360 Planarity : 0.004 0.035 3724 Dihedral : 5.289 27.943 2984 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.29 % Favored : 92.17 % Rotamer: Outliers : 1.49 % Allowed : 9.81 % Favored : 88.70 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.14), residues: 2632 helix: -1.73 (0.14), residues: 1106 sheet: -2.21 (0.21), residues: 490 loop : -2.32 (0.16), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 122 PHE 0.016 0.001 PHE O 2 TYR 0.015 0.001 TYR B 17 ARG 0.002 0.000 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 459 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 426 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7196 (ttmm) cc_final: 0.6852 (tttt) REVERT: A 108 LYS cc_start: 0.8213 (tptm) cc_final: 0.7675 (tppt) REVERT: B 108 LYS cc_start: 0.8318 (tptm) cc_final: 0.7738 (tppt) REVERT: B 118 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6738 (mm-30) REVERT: C 108 LYS cc_start: 0.8379 (tptm) cc_final: 0.7840 (tppt) REVERT: C 118 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7070 (mm-30) REVERT: C 151 LYS cc_start: 0.7451 (tppp) cc_final: 0.7175 (mttt) REVERT: C 165 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7078 (mt-10) REVERT: D 78 ASP cc_start: 0.6143 (m-30) cc_final: 0.5904 (m-30) REVERT: D 84 LYS cc_start: 0.6942 (ttmm) cc_final: 0.6652 (tttt) REVERT: D 108 LYS cc_start: 0.8293 (tptm) cc_final: 0.7685 (tppt) REVERT: E 84 LYS cc_start: 0.6518 (ttmm) cc_final: 0.6283 (tttt) REVERT: E 108 LYS cc_start: 0.8356 (tptm) cc_final: 0.7867 (tppt) REVERT: F 84 LYS cc_start: 0.7106 (ttmm) cc_final: 0.6830 (tttt) REVERT: F 108 LYS cc_start: 0.8177 (tptm) cc_final: 0.7736 (tppt) REVERT: F 186 ASP cc_start: 0.7389 (m-30) cc_final: 0.6904 (m-30) REVERT: G 151 LYS cc_start: 0.7104 (mtpp) cc_final: 0.6661 (mttt) REVERT: I 84 LYS cc_start: 0.7381 (ttmm) cc_final: 0.7064 (tttt) REVERT: I 89 THR cc_start: 0.7341 (p) cc_final: 0.7080 (p) REVERT: I 108 LYS cc_start: 0.8383 (tptm) cc_final: 0.7754 (tppt) REVERT: J 84 LYS cc_start: 0.7028 (ttmm) cc_final: 0.6724 (tttt) REVERT: J 108 LYS cc_start: 0.8428 (tptm) cc_final: 0.7979 (tppt) REVERT: J 110 LYS cc_start: 0.6098 (mttp) cc_final: 0.5864 (mtmm) REVERT: K 108 LYS cc_start: 0.8264 (tptm) cc_final: 0.7778 (tppt) REVERT: L 108 LYS cc_start: 0.8343 (tptm) cc_final: 0.7884 (tppt) REVERT: M 33 SER cc_start: 0.8056 (t) cc_final: 0.7839 (t) REVERT: M 84 LYS cc_start: 0.7095 (ttmm) cc_final: 0.6737 (tttt) REVERT: N 108 LYS cc_start: 0.8316 (tptm) cc_final: 0.7822 (tppt) REVERT: H 84 LYS cc_start: 0.7120 (ttmm) cc_final: 0.6781 (tttm) REVERT: H 108 LYS cc_start: 0.8356 (tptm) cc_final: 0.7868 (tppt) REVERT: H 165 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6997 (mt-10) outliers start: 33 outliers final: 16 residues processed: 432 average time/residue: 0.8201 time to fit residues: 508.9383 Evaluate side-chains 420 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 404 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain U residue 3 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 21280 Z= 0.359 Angle : 1.432 23.524 28658 Z= 0.770 Chirality : 0.253 1.769 3360 Planarity : 0.004 0.039 3724 Dihedral : 6.027 54.451 2982 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.81 % Favored : 90.65 % Rotamer: Outliers : 1.49 % Allowed : 12.07 % Favored : 86.44 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % 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: -2.91 (0.15), residues: 2632 helix: -1.54 (0.15), residues: 1078 sheet: -1.93 (0.23), residues: 462 loop : -2.17 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 122 PHE 0.013 0.001 PHE O 2 TYR 0.015 0.001 TYR E 17 ARG 0.007 0.000 ARG K 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 467 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 434 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7130 (ttmm) cc_final: 0.6727 (tttt) REVERT: A 108 LYS cc_start: 0.8251 (tptm) cc_final: 0.7790 (tppt) REVERT: B 108 LYS cc_start: 0.8355 (tptm) cc_final: 0.7777 (tppt) REVERT: C 84 LYS cc_start: 0.7010 (ttmm) cc_final: 0.6711 (tttm) REVERT: C 108 LYS cc_start: 0.8391 (tptm) cc_final: 0.7798 (tppt) REVERT: C 116 ASN cc_start: 0.6935 (OUTLIER) cc_final: 0.6403 (p0) REVERT: C 136 GLU cc_start: 0.6017 (tt0) cc_final: 0.5750 (tt0) REVERT: D 33 SER cc_start: 0.8147 (t) cc_final: 0.7940 (t) REVERT: D 84 LYS cc_start: 0.7025 (ttmm) cc_final: 0.6718 (tttt) REVERT: D 108 LYS cc_start: 0.8346 (tptm) cc_final: 0.7706 (tppt) REVERT: E 84 LYS cc_start: 0.6920 (ttmm) cc_final: 0.6661 (tttt) REVERT: E 108 LYS cc_start: 0.8288 (tptm) cc_final: 0.7823 (tppt) REVERT: F 84 LYS cc_start: 0.6944 (ttmm) cc_final: 0.6632 (tttt) REVERT: F 178 GLU cc_start: 0.6554 (mm-30) cc_final: 0.6109 (mt-10) REVERT: F 186 ASP cc_start: 0.7306 (m-30) cc_final: 0.6843 (m-30) REVERT: G 56 GLU cc_start: 0.7204 (pm20) cc_final: 0.6734 (pm20) REVERT: G 84 LYS cc_start: 0.7095 (ttmm) cc_final: 0.6828 (tttm) REVERT: G 151 LYS cc_start: 0.7356 (mtpp) cc_final: 0.6931 (mttt) REVERT: I 84 LYS cc_start: 0.7261 (ttmm) cc_final: 0.6936 (tttt) REVERT: I 108 LYS cc_start: 0.8375 (tptm) cc_final: 0.7710 (tppt) REVERT: J 33 SER cc_start: 0.8031 (t) cc_final: 0.7580 (p) REVERT: J 84 LYS cc_start: 0.7187 (ttmm) cc_final: 0.6935 (mtpt) REVERT: J 108 LYS cc_start: 0.8444 (tptm) cc_final: 0.7973 (tppt) REVERT: J 110 LYS cc_start: 0.6239 (mttp) cc_final: 0.5949 (mtmm) REVERT: K 84 LYS cc_start: 0.7202 (ttmm) cc_final: 0.6887 (tttt) REVERT: K 98 MET cc_start: 0.7337 (mmt) cc_final: 0.6891 (mmt) REVERT: K 108 LYS cc_start: 0.8024 (tptm) cc_final: 0.7603 (tppt) REVERT: K 178 GLU cc_start: 0.6294 (mm-30) cc_final: 0.6024 (mt-10) REVERT: L 33 SER cc_start: 0.8205 (t) cc_final: 0.8004 (t) REVERT: L 108 LYS cc_start: 0.8305 (tptm) cc_final: 0.7818 (tppt) REVERT: M 33 SER cc_start: 0.7919 (t) cc_final: 0.7710 (t) REVERT: M 84 LYS cc_start: 0.7136 (ttmm) cc_final: 0.6786 (tttt) REVERT: N 108 LYS cc_start: 0.8304 (tptm) cc_final: 0.7665 (tppt) REVERT: H 58 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: H 84 LYS cc_start: 0.7082 (ttmm) cc_final: 0.6774 (tttm) REVERT: H 108 LYS cc_start: 0.8307 (tptm) cc_final: 0.7762 (tppt) REVERT: H 165 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7033 (mt-10) REVERT: H 178 GLU cc_start: 0.6421 (mm-30) cc_final: 0.6016 (mt-10) outliers start: 33 outliers final: 22 residues processed: 445 average time/residue: 0.9026 time to fit residues: 564.9435 Evaluate side-chains 434 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 410 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain P residue 3 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN D 41 ASN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN K 41 ASN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21280 Z= 0.237 Angle : 1.407 24.095 28658 Z= 0.759 Chirality : 0.253 1.709 3360 Planarity : 0.004 0.036 3724 Dihedral : 5.481 38.674 2982 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.33 % Favored : 92.14 % Rotamer: Outliers : 0.90 % Allowed : 13.02 % Favored : 86.08 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % 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: -2.60 (0.15), residues: 2632 helix: -1.37 (0.15), residues: 1106 sheet: -1.79 (0.23), residues: 462 loop : -1.89 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS J 122 PHE 0.009 0.001 PHE T 2 TYR 0.012 0.001 TYR J 17 ARG 0.004 0.000 ARG K 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 430 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 410 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7074 (ttmm) cc_final: 0.6715 (tttt) REVERT: A 98 MET cc_start: 0.6736 (mmt) cc_final: 0.6377 (mmt) REVERT: A 108 LYS cc_start: 0.8108 (tptm) cc_final: 0.7626 (tppt) REVERT: A 151 LYS cc_start: 0.7200 (mttt) cc_final: 0.6921 (mtpt) REVERT: B 108 LYS cc_start: 0.8307 (tptm) cc_final: 0.7647 (tppt) REVERT: C 8 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.5873 (tt0) REVERT: C 84 LYS cc_start: 0.6876 (ttmm) cc_final: 0.6591 (tttm) REVERT: C 108 LYS cc_start: 0.8385 (tptm) cc_final: 0.7847 (tppt) REVERT: C 116 ASN cc_start: 0.7030 (OUTLIER) cc_final: 0.6538 (p0) REVERT: C 165 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7000 (mt-10) REVERT: D 33 SER cc_start: 0.8114 (t) cc_final: 0.7852 (t) REVERT: D 84 LYS cc_start: 0.6923 (ttmm) cc_final: 0.6589 (tttt) REVERT: D 108 LYS cc_start: 0.8371 (tptm) cc_final: 0.7718 (tppt) REVERT: E 84 LYS cc_start: 0.6860 (ttmm) cc_final: 0.6631 (tttt) REVERT: E 108 LYS cc_start: 0.8322 (tptm) cc_final: 0.7864 (tppt) REVERT: F 84 LYS cc_start: 0.7061 (ttmm) cc_final: 0.6768 (tttt) REVERT: F 178 GLU cc_start: 0.6561 (mm-30) cc_final: 0.6108 (mt-10) REVERT: F 186 ASP cc_start: 0.7359 (m-30) cc_final: 0.6900 (m-30) REVERT: G 56 GLU cc_start: 0.7170 (pm20) cc_final: 0.6654 (pm20) REVERT: G 84 LYS cc_start: 0.7004 (ttmm) cc_final: 0.6789 (tttt) REVERT: G 151 LYS cc_start: 0.7323 (mtpp) cc_final: 0.6906 (mttt) REVERT: I 20 TYR cc_start: 0.7428 (m-80) cc_final: 0.7063 (m-10) REVERT: I 84 LYS cc_start: 0.7272 (ttmm) cc_final: 0.6956 (tttt) REVERT: I 108 LYS cc_start: 0.8356 (tptm) cc_final: 0.7672 (tppt) REVERT: I 177 GLU cc_start: 0.6459 (tm-30) cc_final: 0.6110 (tm-30) REVERT: J 84 LYS cc_start: 0.7120 (ttmm) cc_final: 0.6792 (tttt) REVERT: J 108 LYS cc_start: 0.8404 (tptm) cc_final: 0.7974 (tppt) REVERT: J 110 LYS cc_start: 0.6223 (mttp) cc_final: 0.5952 (mtmm) REVERT: K 84 LYS cc_start: 0.6890 (ttmm) cc_final: 0.6574 (tttt) REVERT: K 98 MET cc_start: 0.7364 (mmt) cc_final: 0.7040 (mmt) REVERT: K 108 LYS cc_start: 0.8068 (tptm) cc_final: 0.7599 (tppt) REVERT: K 178 GLU cc_start: 0.6309 (mm-30) cc_final: 0.6042 (mt-10) REVERT: L 108 LYS cc_start: 0.8303 (tptm) cc_final: 0.7815 (tppt) REVERT: M 33 SER cc_start: 0.7957 (t) cc_final: 0.7738 (t) REVERT: M 84 LYS cc_start: 0.7048 (ttmm) cc_final: 0.6707 (tttt) REVERT: N 108 LYS cc_start: 0.8311 (tptm) cc_final: 0.7636 (tppt) REVERT: H 8 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.5813 (tt0) REVERT: H 58 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7323 (tt0) REVERT: H 84 LYS cc_start: 0.6849 (ttmm) cc_final: 0.6561 (tttm) REVERT: H 108 LYS cc_start: 0.8303 (tptm) cc_final: 0.7722 (tppt) REVERT: H 165 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6928 (mt-10) REVERT: H 178 GLU cc_start: 0.6468 (mm-30) cc_final: 0.5959 (mt-10) outliers start: 20 outliers final: 14 residues processed: 424 average time/residue: 0.8556 time to fit residues: 515.8113 Evaluate side-chains 417 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 399 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 58 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 0.0970 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21280 Z= 0.293 Angle : 1.417 23.933 28658 Z= 0.763 Chirality : 0.254 1.752 3360 Planarity : 0.004 0.037 3724 Dihedral : 5.762 49.566 2982 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.31 % Favored : 90.16 % Rotamer: Outliers : 1.36 % Allowed : 13.07 % Favored : 85.58 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % 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: -2.46 (0.15), residues: 2632 helix: -1.21 (0.15), residues: 1078 sheet: -1.68 (0.23), residues: 462 loop : -1.89 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 122 PHE 0.010 0.001 PHE T 2 TYR 0.013 0.001 TYR J 17 ARG 0.004 0.000 ARG N 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 422 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 392 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6314 (tt0) REVERT: A 84 LYS cc_start: 0.7120 (ttmm) cc_final: 0.6754 (tttt) REVERT: A 98 MET cc_start: 0.6952 (mmt) cc_final: 0.6671 (mmt) REVERT: A 108 LYS cc_start: 0.8087 (tptm) cc_final: 0.7514 (tppt) REVERT: A 151 LYS cc_start: 0.7175 (mttt) cc_final: 0.6910 (mtpt) REVERT: B 8 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.5575 (tt0) REVERT: B 108 LYS cc_start: 0.8250 (tptm) cc_final: 0.7557 (tppt) REVERT: C 8 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.5882 (tt0) REVERT: C 84 LYS cc_start: 0.6983 (ttmm) cc_final: 0.6696 (tttm) REVERT: C 108 LYS cc_start: 0.8365 (tptm) cc_final: 0.7798 (tppt) REVERT: C 116 ASN cc_start: 0.7020 (OUTLIER) cc_final: 0.6562 (p0) REVERT: C 165 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6984 (mt-10) REVERT: D 8 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.5552 (tt0) REVERT: D 33 SER cc_start: 0.8114 (t) cc_final: 0.7891 (t) REVERT: D 84 LYS cc_start: 0.6939 (ttmm) cc_final: 0.6630 (tttt) REVERT: E 84 LYS cc_start: 0.6966 (ttmm) cc_final: 0.6744 (tttt) REVERT: E 108 LYS cc_start: 0.8232 (tptm) cc_final: 0.7743 (tppt) REVERT: F 8 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.5993 (tt0) REVERT: F 178 GLU cc_start: 0.6561 (mm-30) cc_final: 0.6107 (mt-10) REVERT: F 186 ASP cc_start: 0.7392 (m-30) cc_final: 0.6964 (m-30) REVERT: G 8 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.5737 (tt0) REVERT: G 84 LYS cc_start: 0.7026 (ttmm) cc_final: 0.6799 (tttt) REVERT: G 151 LYS cc_start: 0.7309 (mtpp) cc_final: 0.6901 (mttt) REVERT: I 8 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.5609 (tt0) REVERT: I 20 TYR cc_start: 0.7432 (m-80) cc_final: 0.7103 (m-10) REVERT: I 84 LYS cc_start: 0.7266 (ttmm) cc_final: 0.6912 (tttt) REVERT: I 108 LYS cc_start: 0.8332 (tptm) cc_final: 0.7643 (tppt) REVERT: I 177 GLU cc_start: 0.6505 (tm-30) cc_final: 0.6167 (tm-30) REVERT: J 8 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.5636 (tt0) REVERT: J 84 LYS cc_start: 0.7213 (ttmm) cc_final: 0.6898 (tttt) REVERT: J 108 LYS cc_start: 0.8398 (tptm) cc_final: 0.7955 (tppt) REVERT: J 110 LYS cc_start: 0.6211 (mttp) cc_final: 0.5933 (mtmm) REVERT: K 84 LYS cc_start: 0.7002 (ttmm) cc_final: 0.6676 (tttt) REVERT: K 178 GLU cc_start: 0.6331 (mm-30) cc_final: 0.6040 (mt-10) REVERT: L 8 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.5877 (tt0) REVERT: L 98 MET cc_start: 0.7057 (mmt) cc_final: 0.6469 (tpt) REVERT: L 108 LYS cc_start: 0.8322 (tptm) cc_final: 0.7787 (tppt) REVERT: M 8 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.5839 (tt0) REVERT: M 33 SER cc_start: 0.7879 (t) cc_final: 0.7667 (t) REVERT: M 84 LYS cc_start: 0.7084 (ttmm) cc_final: 0.6726 (tttt) REVERT: N 8 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.5548 (tt0) REVERT: N 108 LYS cc_start: 0.8292 (tptm) cc_final: 0.7696 (tppt) REVERT: H 8 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.5828 (tt0) REVERT: H 58 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: H 84 LYS cc_start: 0.6975 (ttmm) cc_final: 0.6686 (tttm) REVERT: H 108 LYS cc_start: 0.8317 (tptm) cc_final: 0.7712 (tppt) REVERT: H 165 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6784 (mt-10) REVERT: H 178 GLU cc_start: 0.6482 (mm-30) cc_final: 0.6002 (mt-10) outliers start: 30 outliers final: 12 residues processed: 414 average time/residue: 0.8256 time to fit residues: 488.2869 Evaluate side-chains 407 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 381 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain L residue 8 GLU Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 8 GLU Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 58 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21280 Z= 0.283 Angle : 1.417 24.089 28658 Z= 0.764 Chirality : 0.254 1.745 3360 Planarity : 0.004 0.036 3724 Dihedral : 5.717 49.784 2982 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.47 % Favored : 91.00 % Rotamer: Outliers : 1.40 % Allowed : 13.29 % Favored : 85.31 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % 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: -2.37 (0.15), residues: 2632 helix: -1.15 (0.15), residues: 1078 sheet: -1.63 (0.23), residues: 462 loop : -1.83 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS J 122 PHE 0.010 0.001 PHE T 2 TYR 0.012 0.001 TYR E 17 ARG 0.003 0.000 ARG N 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 404 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 373 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.5737 (tt0) REVERT: A 84 LYS cc_start: 0.7080 (ttmm) cc_final: 0.6714 (tttt) REVERT: B 8 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.5538 (tt0) REVERT: B 108 LYS cc_start: 0.8257 (tptm) cc_final: 0.7551 (tppt) REVERT: C 8 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.5926 (tt0) REVERT: C 108 LYS cc_start: 0.8400 (tptm) cc_final: 0.7852 (tppt) REVERT: C 116 ASN cc_start: 0.7023 (OUTLIER) cc_final: 0.6539 (p0) REVERT: C 165 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6966 (mt-10) REVERT: D 33 SER cc_start: 0.7975 (t) cc_final: 0.7720 (t) REVERT: D 84 LYS cc_start: 0.6908 (ttmm) cc_final: 0.6605 (tttt) REVERT: E 8 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.5674 (tt0) REVERT: E 84 LYS cc_start: 0.6830 (ttmm) cc_final: 0.6614 (tttt) REVERT: E 108 LYS cc_start: 0.8211 (tptm) cc_final: 0.7707 (tppt) REVERT: F 8 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6003 (tt0) REVERT: F 178 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6087 (mt-10) REVERT: F 186 ASP cc_start: 0.7436 (m-30) cc_final: 0.7027 (m-30) REVERT: G 8 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.5700 (tt0) REVERT: G 84 LYS cc_start: 0.6932 (ttmm) cc_final: 0.6722 (tttt) REVERT: G 151 LYS cc_start: 0.7296 (mtpp) cc_final: 0.6895 (mttt) REVERT: I 20 TYR cc_start: 0.7194 (m-80) cc_final: 0.6896 (m-10) REVERT: I 84 LYS cc_start: 0.7268 (ttmm) cc_final: 0.6948 (tttt) REVERT: I 108 LYS cc_start: 0.8252 (tptm) cc_final: 0.7543 (tppt) REVERT: I 177 GLU cc_start: 0.6477 (tm-30) cc_final: 0.6156 (tm-30) REVERT: J 8 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.5751 (tt0) REVERT: J 84 LYS cc_start: 0.7178 (ttmm) cc_final: 0.6854 (tttt) REVERT: J 108 LYS cc_start: 0.8376 (tptm) cc_final: 0.7918 (tppt) REVERT: J 110 LYS cc_start: 0.6100 (mttp) cc_final: 0.5814 (mtmm) REVERT: J 177 GLU cc_start: 0.6110 (tm-30) cc_final: 0.5788 (tm-30) REVERT: K 84 LYS cc_start: 0.7058 (ttmm) cc_final: 0.6743 (tttt) REVERT: K 178 GLU cc_start: 0.6339 (mm-30) cc_final: 0.6021 (mt-10) REVERT: L 8 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.5779 (tt0) REVERT: L 54 ASP cc_start: 0.7149 (t0) cc_final: 0.6919 (t0) REVERT: L 108 LYS cc_start: 0.8268 (tptm) cc_final: 0.7690 (tppt) REVERT: M 84 LYS cc_start: 0.7000 (ttmm) cc_final: 0.6666 (tttt) REVERT: N 8 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.5548 (tt0) REVERT: N 108 LYS cc_start: 0.8243 (tptm) cc_final: 0.7525 (tppt) REVERT: H 8 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.5860 (tt0) REVERT: H 58 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: H 108 LYS cc_start: 0.8334 (tptm) cc_final: 0.7807 (tppt) REVERT: H 165 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6758 (mt-10) REVERT: H 178 GLU cc_start: 0.6478 (mm-30) cc_final: 0.5991 (mt-10) outliers start: 31 outliers final: 18 residues processed: 396 average time/residue: 0.8340 time to fit residues: 472.8833 Evaluate side-chains 398 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 368 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain L residue 8 GLU Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 8 GLU Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 58 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21280 Z= 0.270 Angle : 1.415 24.181 28658 Z= 0.763 Chirality : 0.254 1.742 3360 Planarity : 0.004 0.036 3724 Dihedral : 5.657 48.813 2982 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.42 % Favored : 90.05 % Rotamer: Outliers : 1.45 % Allowed : 13.61 % Favored : 84.95 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % 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: -2.32 (0.16), residues: 2632 helix: -1.15 (0.15), residues: 1106 sheet: -1.59 (0.24), residues: 462 loop : -1.76 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 122 PHE 0.009 0.001 PHE O 2 TYR 0.012 0.001 TYR E 17 ARG 0.003 0.000 ARG N 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 399 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 367 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.5695 (tt0) REVERT: A 84 LYS cc_start: 0.7047 (ttmm) cc_final: 0.6682 (tttt) REVERT: B 108 LYS cc_start: 0.8246 (tptm) cc_final: 0.7534 (tppt) REVERT: C 8 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.5887 (tt0) REVERT: C 108 LYS cc_start: 0.8367 (tptm) cc_final: 0.7835 (tppt) REVERT: C 116 ASN cc_start: 0.7004 (OUTLIER) cc_final: 0.6541 (p0) REVERT: C 165 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6975 (mt-10) REVERT: D 33 SER cc_start: 0.7943 (t) cc_final: 0.7691 (t) REVERT: E 8 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.5670 (tt0) REVERT: E 84 LYS cc_start: 0.6875 (ttmm) cc_final: 0.6656 (tttt) REVERT: E 108 LYS cc_start: 0.8238 (tptm) cc_final: 0.7732 (tppt) REVERT: F 8 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6001 (tt0) REVERT: F 178 GLU cc_start: 0.6539 (mm-30) cc_final: 0.6091 (mt-10) REVERT: F 186 ASP cc_start: 0.7447 (m-30) cc_final: 0.7044 (m-30) REVERT: G 8 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.5704 (tt0) REVERT: G 84 LYS cc_start: 0.6994 (ttmm) cc_final: 0.6777 (tttt) REVERT: G 151 LYS cc_start: 0.7259 (mtpp) cc_final: 0.6862 (mttt) REVERT: I 20 TYR cc_start: 0.7176 (m-80) cc_final: 0.6902 (m-10) REVERT: I 84 LYS cc_start: 0.7255 (ttmm) cc_final: 0.6935 (tttt) REVERT: I 108 LYS cc_start: 0.8160 (tptm) cc_final: 0.7540 (tppt) REVERT: I 177 GLU cc_start: 0.6501 (tm-30) cc_final: 0.6171 (tm-30) REVERT: J 8 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.5622 (tt0) REVERT: J 84 LYS cc_start: 0.7252 (ttmm) cc_final: 0.6933 (tttt) REVERT: J 108 LYS cc_start: 0.8380 (tptm) cc_final: 0.7895 (tppt) REVERT: J 110 LYS cc_start: 0.6096 (mttp) cc_final: 0.5822 (mtmm) REVERT: J 177 GLU cc_start: 0.6134 (tm-30) cc_final: 0.5809 (tm-30) REVERT: K 84 LYS cc_start: 0.7109 (ttmm) cc_final: 0.6794 (tttt) REVERT: K 178 GLU cc_start: 0.6339 (mm-30) cc_final: 0.6034 (mt-10) REVERT: L 54 ASP cc_start: 0.7054 (t0) cc_final: 0.6827 (t0) REVERT: L 98 MET cc_start: 0.6883 (tpt) cc_final: 0.6444 (tpt) REVERT: L 108 LYS cc_start: 0.8307 (tptm) cc_final: 0.7717 (tppt) REVERT: M 84 LYS cc_start: 0.7023 (ttmm) cc_final: 0.6679 (tttt) REVERT: N 108 LYS cc_start: 0.8227 (tptm) cc_final: 0.7486 (tppt) REVERT: H 8 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.5836 (tt0) REVERT: H 58 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: H 108 LYS cc_start: 0.8358 (tptm) cc_final: 0.7831 (tppt) REVERT: H 165 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6746 (mt-10) REVERT: H 178 GLU cc_start: 0.6475 (mm-30) cc_final: 0.5987 (mt-10) outliers start: 32 outliers final: 21 residues processed: 392 average time/residue: 0.8468 time to fit residues: 481.9914 Evaluate side-chains 390 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 360 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain L residue 8 GLU Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 8 GLU Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 58 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 225 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21280 Z= 0.198 Angle : 1.405 24.744 28658 Z= 0.759 Chirality : 0.255 1.711 3360 Planarity : 0.003 0.032 3724 Dihedral : 4.998 30.300 2982 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.69 % Favored : 92.78 % Rotamer: Outliers : 1.31 % Allowed : 13.83 % Favored : 84.86 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % 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: -1.97 (0.16), residues: 2632 helix: -1.00 (0.16), residues: 1008 sheet: -1.51 (0.24), residues: 462 loop : -1.34 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS J 122 PHE 0.005 0.001 PHE T 2 TYR 0.009 0.001 TYR J 17 ARG 0.003 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 394 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 365 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.5692 (tt0) REVERT: A 84 LYS cc_start: 0.6972 (ttmm) cc_final: 0.6616 (tttt) REVERT: B 8 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.5541 (tt0) REVERT: B 108 LYS cc_start: 0.8248 (tptm) cc_final: 0.7535 (tppt) REVERT: B 120 MET cc_start: 0.7722 (ttp) cc_final: 0.7079 (tmm) REVERT: C 8 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.5891 (tt0) REVERT: C 108 LYS cc_start: 0.8363 (tptm) cc_final: 0.7802 (tppt) REVERT: C 116 ASN cc_start: 0.6848 (OUTLIER) cc_final: 0.6423 (p0) REVERT: C 165 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6903 (mt-10) REVERT: E 8 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.5662 (tt0) REVERT: E 108 LYS cc_start: 0.8237 (tptm) cc_final: 0.7719 (tppt) REVERT: F 8 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.5988 (tt0) REVERT: F 178 GLU cc_start: 0.6538 (mm-30) cc_final: 0.6084 (mt-10) REVERT: F 186 ASP cc_start: 0.7433 (m-30) cc_final: 0.6994 (m-30) REVERT: G 8 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.5716 (tt0) REVERT: G 84 LYS cc_start: 0.6874 (ttmm) cc_final: 0.6670 (tttt) REVERT: G 151 LYS cc_start: 0.6944 (mtpp) cc_final: 0.6612 (mttt) REVERT: I 20 TYR cc_start: 0.7230 (m-80) cc_final: 0.6931 (m-10) REVERT: I 84 LYS cc_start: 0.7190 (ttmm) cc_final: 0.6895 (tttt) REVERT: I 89 THR cc_start: 0.7477 (p) cc_final: 0.7227 (p) REVERT: I 108 LYS cc_start: 0.8178 (tptm) cc_final: 0.7540 (tppt) REVERT: I 177 GLU cc_start: 0.6437 (tm-30) cc_final: 0.6123 (tm-30) REVERT: J 84 LYS cc_start: 0.7060 (ttmm) cc_final: 0.6772 (tttt) REVERT: J 108 LYS cc_start: 0.8393 (tptm) cc_final: 0.7902 (tppt) REVERT: J 110 LYS cc_start: 0.6107 (mttp) cc_final: 0.5848 (mtmm) REVERT: J 177 GLU cc_start: 0.6138 (tm-30) cc_final: 0.5810 (tm-30) REVERT: K 178 GLU cc_start: 0.6438 (mm-30) cc_final: 0.6080 (mt-10) REVERT: L 8 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.5718 (tt0) REVERT: L 98 MET cc_start: 0.6905 (tpt) cc_final: 0.6495 (tpt) REVERT: L 108 LYS cc_start: 0.8303 (tptm) cc_final: 0.7707 (tppt) REVERT: M 84 LYS cc_start: 0.6970 (ttmm) cc_final: 0.6627 (tttt) REVERT: N 8 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.5543 (tt0) REVERT: N 108 LYS cc_start: 0.8209 (tptm) cc_final: 0.7448 (tppt) REVERT: N 120 MET cc_start: 0.7719 (ttp) cc_final: 0.7090 (tmm) REVERT: H 108 LYS cc_start: 0.8185 (tptm) cc_final: 0.7685 (tppt) REVERT: H 116 ASN cc_start: 0.6578 (p0) cc_final: 0.6303 (p0) REVERT: H 178 GLU cc_start: 0.6459 (mm-30) cc_final: 0.5977 (mt-10) outliers start: 29 outliers final: 18 residues processed: 383 average time/residue: 0.8448 time to fit residues: 463.5245 Evaluate side-chains 382 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 355 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain L residue 8 GLU Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 8 GLU Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 116 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21280 Z= 0.203 Angle : 1.403 24.649 28658 Z= 0.758 Chirality : 0.254 1.723 3360 Planarity : 0.003 0.033 3724 Dihedral : 4.979 32.597 2982 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.98 % Favored : 91.49 % Rotamer: Outliers : 1.27 % Allowed : 13.83 % Favored : 84.90 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % 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: -1.76 (0.16), residues: 2632 helix: -0.75 (0.17), residues: 1008 sheet: -1.39 (0.25), residues: 434 loop : -1.32 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS J 122 PHE 0.005 0.001 PHE T 2 TYR 0.010 0.001 TYR E 17 ARG 0.002 0.000 ARG N 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 387 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 359 time to evaluate : 3.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.5620 (tt0) REVERT: A 84 LYS cc_start: 0.6991 (ttmm) cc_final: 0.6640 (tttt) REVERT: B 8 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.5500 (tt0) REVERT: B 108 LYS cc_start: 0.8236 (tptm) cc_final: 0.7522 (tppt) REVERT: B 120 MET cc_start: 0.7717 (ttp) cc_final: 0.7091 (tmm) REVERT: C 8 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.5853 (tt0) REVERT: C 108 LYS cc_start: 0.8201 (tptm) cc_final: 0.7664 (tppt) REVERT: C 116 ASN cc_start: 0.6824 (OUTLIER) cc_final: 0.6368 (p0) REVERT: E 8 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.5615 (tt0) REVERT: E 108 LYS cc_start: 0.8230 (tptm) cc_final: 0.7717 (tppt) REVERT: F 8 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.5954 (tt0) REVERT: F 178 GLU cc_start: 0.6529 (mm-30) cc_final: 0.6050 (mt-10) REVERT: F 186 ASP cc_start: 0.7443 (m-30) cc_final: 0.7041 (m-30) REVERT: G 8 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.5717 (tt0) REVERT: G 84 LYS cc_start: 0.6897 (ttmm) cc_final: 0.6697 (tttt) REVERT: G 151 LYS cc_start: 0.6907 (mtpp) cc_final: 0.6575 (mttt) REVERT: I 20 TYR cc_start: 0.7181 (m-80) cc_final: 0.6887 (m-10) REVERT: I 84 LYS cc_start: 0.7165 (ttmm) cc_final: 0.6864 (tttt) REVERT: I 89 THR cc_start: 0.7441 (p) cc_final: 0.7187 (p) REVERT: I 108 LYS cc_start: 0.8166 (tptm) cc_final: 0.7527 (tppt) REVERT: I 177 GLU cc_start: 0.6438 (tm-30) cc_final: 0.6126 (tm-30) REVERT: J 84 LYS cc_start: 0.7110 (ttmm) cc_final: 0.6894 (ttpt) REVERT: J 108 LYS cc_start: 0.8445 (tptm) cc_final: 0.7962 (tppt) REVERT: J 110 LYS cc_start: 0.6104 (mttp) cc_final: 0.5846 (mtmm) REVERT: J 177 GLU cc_start: 0.6125 (tm-30) cc_final: 0.5800 (tm-30) REVERT: K 178 GLU cc_start: 0.6401 (mm-30) cc_final: 0.6042 (mt-10) REVERT: L 8 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.5653 (tt0) REVERT: L 108 LYS cc_start: 0.8333 (tptm) cc_final: 0.7744 (tppt) REVERT: M 8 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.5708 (tt0) REVERT: M 84 LYS cc_start: 0.6978 (ttmm) cc_final: 0.6663 (tttt) REVERT: N 8 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.5425 (tt0) REVERT: N 108 LYS cc_start: 0.8105 (tptm) cc_final: 0.7437 (tppt) REVERT: N 120 MET cc_start: 0.7685 (ttp) cc_final: 0.7053 (tmm) REVERT: H 8 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.5651 (tt0) REVERT: H 108 LYS cc_start: 0.8169 (tptm) cc_final: 0.7671 (tppt) REVERT: H 116 ASN cc_start: 0.6557 (p0) cc_final: 0.6326 (p0) REVERT: H 178 GLU cc_start: 0.6470 (mm-30) cc_final: 0.5984 (mt-10) outliers start: 28 outliers final: 17 residues processed: 378 average time/residue: 0.8346 time to fit residues: 453.5389 Evaluate side-chains 385 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 357 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain L residue 8 GLU Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 8 GLU Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain H residue 8 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 200 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.0370 chunk 175 optimal weight: 3.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.127453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.105097 restraints weight = 67973.888| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.67 r_work: 0.3098 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21280 Z= 0.191 Angle : 1.401 24.819 28658 Z= 0.757 Chirality : 0.255 1.702 3360 Planarity : 0.003 0.031 3724 Dihedral : 4.705 26.236 2982 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.27 % Favored : 93.35 % Rotamer: Outliers : 1.31 % Allowed : 13.83 % Favored : 84.86 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % 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 (0.16), residues: 2632 helix: -0.54 (0.17), residues: 1008 sheet: -0.75 (0.23), residues: 532 loop : -1.35 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS J 122 PHE 0.004 0.000 PHE T 2 TYR 0.009 0.001 TYR E 17 ARG 0.002 0.000 ARG C 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9965.16 seconds wall clock time: 179 minutes 50.88 seconds (10790.88 seconds total)