Starting phenix.real_space_refine on Fri Mar 15 10:40:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sas_24955/03_2024/7sas_24955.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sas_24955/03_2024/7sas_24955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sas_24955/03_2024/7sas_24955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sas_24955/03_2024/7sas_24955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sas_24955/03_2024/7sas_24955.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sas_24955/03_2024/7sas_24955.pdb" } resolution = 3.7 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 7260 2.51 5 N 1770 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 122": "OD1" <-> "OD2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "C ASP 122": "OD1" <-> "OD2" Residue "C TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "D ASP 122": "OD1" <-> "OD2" Residue "D TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "E ASP 122": "OD1" <-> "OD2" Residue "E TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "G ASP 122": "OD1" <-> "OD2" Residue "G TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "H ASP 122": "OD1" <-> "OD2" Residue "H TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "I ASP 122": "OD1" <-> "OD2" Residue "I TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 205": "OE1" <-> "OE2" Residue "J ASP 122": "OD1" <-> "OD2" Residue "J TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 205": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11420 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "C" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "D" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "E" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "F" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "G" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "H" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "I" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "J" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.40, per 1000 atoms: 0.56 Number of scatterers: 11420 At special positions: 0 Unit cell: (155.1, 190.3, 49.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2320 8.00 N 1770 7.00 C 7260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 253 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 214 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS G 214 " - pdb=" SG CYS G 253 " distance=2.03 Simple disulfide: pdb=" SG CYS H 214 " - pdb=" SG CYS H 253 " distance=2.03 Simple disulfide: pdb=" SG CYS I 214 " - pdb=" SG CYS I 253 " distance=2.03 Simple disulfide: pdb=" SG CYS J 214 " - pdb=" SG CYS J 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 301 " - " ASN A 151 " " NAG A 302 " - " ASN A 164 " " NAG A 303 " - " ASN A 183 " " NAG A 304 " - " ASN A 145 " " NAG B 301 " - " ASN B 151 " " NAG B 302 " - " ASN B 164 " " NAG B 303 " - " ASN B 183 " " NAG B 304 " - " ASN B 145 " " NAG C 301 " - " ASN C 151 " " NAG C 302 " - " ASN C 164 " " NAG C 303 " - " ASN C 183 " " NAG C 304 " - " ASN C 145 " " NAG D 301 " - " ASN D 151 " " NAG D 302 " - " ASN D 164 " " NAG D 303 " - " ASN D 183 " " NAG D 304 " - " ASN D 145 " " NAG E 301 " - " ASN E 151 " " NAG E 302 " - " ASN E 164 " " NAG E 303 " - " ASN E 183 " " NAG E 304 " - " ASN E 145 " " NAG F 301 " - " ASN F 151 " " NAG F 302 " - " ASN F 164 " " NAG F 303 " - " ASN F 183 " " NAG F 304 " - " ASN F 145 " " NAG G 301 " - " ASN G 151 " " NAG G 302 " - " ASN G 164 " " NAG G 303 " - " ASN G 183 " " NAG G 304 " - " ASN G 145 " " NAG H 301 " - " ASN H 151 " " NAG H 302 " - " ASN H 164 " " NAG H 303 " - " ASN H 183 " " NAG H 304 " - " ASN H 145 " " NAG I 301 " - " ASN I 151 " " NAG I 302 " - " ASN I 164 " " NAG I 303 " - " ASN I 183 " " NAG I 304 " - " ASN I 145 " " NAG J 301 " - " ASN J 151 " " NAG J 302 " - " ASN J 164 " " NAG J 303 " - " ASN J 183 " " NAG J 304 " - " ASN J 145 " Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 1.8 seconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 71.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 122 through 126 removed outlier: 6.647A pdb=" N ASP A 122 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N TYR E 125 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS A 124 " --> pdb=" O TYR E 125 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP E 122 " --> pdb=" O VAL I 123 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N TYR I 125 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS E 124 " --> pdb=" O TYR I 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 129 through 138 removed outlier: 8.961A pdb=" N SER D 130 " --> pdb=" O ALA H 131 " (cutoff:3.500A) removed outlier: 10.147A pdb=" N VAL H 133 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR D 132 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR H 135 " --> pdb=" O TYR D 132 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N SER D 134 " --> pdb=" O TYR H 135 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL H 137 " --> pdb=" O SER D 134 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP D 136 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N SER A 130 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 10.147A pdb=" N VAL D 133 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR A 132 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TYR D 135 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER A 134 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL D 137 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASP A 136 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER E 130 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA A 131 " --> pdb=" O SER E 130 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR E 132 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER I 130 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA E 131 " --> pdb=" O SER I 130 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR I 132 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 142 through 143 removed outlier: 6.474A pdb=" N ILE D 142 " --> pdb=" O TYR H 143 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE A 142 " --> pdb=" O TYR D 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 146 through 160 removed outlier: 6.492A pdb=" N THR D 147 " --> pdb=" O ASN H 148 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU H 150 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR D 149 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE H 152 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN D 151 " --> pdb=" O ILE H 152 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN H 154 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR D 153 " --> pdb=" O ASN H 154 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ASN H 156 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN D 155 " --> pdb=" O ASN H 156 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N TYR H 158 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR D 157 " --> pdb=" O TYR H 158 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL H 160 " --> pdb=" O TYR D 157 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER D 159 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 146 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR E 149 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN A 148 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ASN E 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 150 " --> pdb=" O ASN E 151 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR E 153 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 152 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ASN E 155 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN A 154 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N TYR E 157 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN A 156 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER E 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N TYR A 158 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 163 through 177 removed outlier: 5.706A pdb=" N ASN D 164 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA H 167 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR D 166 " --> pdb=" O ALA H 167 " (cutoff:3.500A) removed outlier: 10.513A pdb=" N VAL H 169 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLN D 168 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N PHE H 171 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N GLN D 170 " --> pdb=" O PHE H 171 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N LYS H 173 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N SER D 172 " --> pdb=" O LYS H 173 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL H 175 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N THR D 174 " --> pdb=" O VAL H 175 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N GLY H 177 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ILE D 176 " --> pdb=" O GLY H 177 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASN A 164 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA D 167 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR A 166 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 10.513A pdb=" N VAL D 169 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLN A 168 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N PHE D 171 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N GLN A 170 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N LYS D 173 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N SER A 172 " --> pdb=" O LYS D 173 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL D 175 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N THR A 174 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N GLY D 177 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N ILE A 176 " --> pdb=" O GLY D 177 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA A 167 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN E 168 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 169 " --> pdb=" O GLN E 168 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN E 170 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE A 171 " --> pdb=" O GLN E 170 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER E 172 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS A 173 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR E 174 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A 175 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE E 176 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY A 177 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA E 167 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN I 168 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL E 169 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN I 170 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE E 171 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER I 172 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS E 173 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR I 174 " --> pdb=" O LYS E 173 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL E 175 " --> pdb=" O THR I 174 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE I 176 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY E 177 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 180 through 187 removed outlier: 7.017A pdb=" N LEU D 181 " --> pdb=" O ARG H 180 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN H 182 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN D 183 " --> pdb=" O ASN H 182 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A 181 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN D 182 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A 183 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N ARG A 180 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N ASN E 183 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN A 182 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N THR E 185 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 184 " --> pdb=" O THR E 185 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE E 187 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 186 " --> pdb=" O ILE E 187 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N ARG E 180 " --> pdb=" O LEU I 181 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N ASN I 183 " --> pdb=" O ARG E 180 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN E 182 " --> pdb=" O ASN I 183 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N THR I 185 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE E 184 " --> pdb=" O THR I 185 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE I 187 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE E 186 " --> pdb=" O ILE I 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 194 through 198 removed outlier: 6.720A pdb=" N ILE A 195 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR E 198 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A 197 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE E 195 " --> pdb=" O ASP I 196 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR I 198 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR E 197 " --> pdb=" O THR I 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 201 through 203 removed outlier: 6.403A pdb=" N VAL D 202 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL A 202 " --> pdb=" O ILE D 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 209 through 230 removed outlier: 7.031A pdb=" N THR D 215 " --> pdb=" O CYS H 214 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU H 216 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE D 217 " --> pdb=" O LEU H 216 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER H 218 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE D 219 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE H 224 " --> pdb=" O ASN D 223 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL D 225 " --> pdb=" O ILE H 224 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU H 226 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N MET D 227 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N MET H 228 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A 215 " --> pdb=" O CYS D 214 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU D 216 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE A 217 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N SER D 218 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 219 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE D 224 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL A 225 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU D 226 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N MET A 227 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N MET D 228 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N MET A 210 " --> pdb=" O TYR E 211 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N PHE E 213 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP A 212 " --> pdb=" O PHE E 213 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N THR E 215 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N CYS A 214 " --> pdb=" O THR E 215 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N ILE E 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N LEU A 216 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ILE E 219 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER A 218 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N VAL E 221 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS A 220 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASN E 223 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N HIS A 222 " --> pdb=" O ASN E 223 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL E 225 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N ILE A 224 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N MET E 227 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N LEU A 226 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N GLN E 229 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N MET A 228 " --> pdb=" O GLN E 229 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N MET E 210 " --> pdb=" O TYR I 211 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N PHE I 213 " --> pdb=" O MET E 210 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP E 212 " --> pdb=" O PHE I 213 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N THR I 215 " --> pdb=" O ASP E 212 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N CYS E 214 " --> pdb=" O THR I 215 " (cutoff:3.500A) removed outlier: 10.806A pdb=" N ILE I 217 " --> pdb=" O CYS E 214 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N LEU E 216 " --> pdb=" O ILE I 217 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N ILE I 219 " --> pdb=" O LEU E 216 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER E 218 " --> pdb=" O ILE I 219 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N VAL I 221 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS E 220 " --> pdb=" O VAL I 221 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ASN I 223 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N HIS E 222 " --> pdb=" O ASN I 223 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL I 225 " --> pdb=" O HIS E 222 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N ILE E 224 " --> pdb=" O VAL I 225 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N MET I 227 " --> pdb=" O ILE E 224 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N LEU E 226 " --> pdb=" O MET I 227 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N GLN I 229 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N MET E 228 " --> pdb=" O GLN I 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 233 through 253 removed outlier: 7.032A pdb=" N VAL H 251 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP D 252 " --> pdb=" O VAL H 251 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS H 253 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL D 251 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP A 252 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS D 253 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR A 233 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N TYR E 236 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR A 235 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N GLY E 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE A 237 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N SER E 240 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N HIS A 239 " --> pdb=" O SER E 240 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N GLN E 242 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU A 241 " --> pdb=" O GLN E 242 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N SER E 244 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 243 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLU E 246 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLN A 245 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N TYR E 248 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG A 247 " --> pdb=" O TYR E 248 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N TYR E 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N GLN A 249 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASP E 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N VAL A 251 " --> pdb=" O ASP E 252 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR E 233 " --> pdb=" O THR I 234 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N TYR I 236 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR E 235 " --> pdb=" O TYR I 236 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N GLY I 238 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE E 237 " --> pdb=" O GLY I 238 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N SER I 240 " --> pdb=" O PHE E 237 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS E 239 " --> pdb=" O SER I 240 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N GLN I 242 " --> pdb=" O HIS E 239 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU E 241 " --> pdb=" O GLN I 242 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N SER I 244 " --> pdb=" O GLU E 241 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE E 243 " --> pdb=" O SER I 244 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLU I 246 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN E 245 " --> pdb=" O GLU I 246 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N TYR I 248 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG E 247 " --> pdb=" O TYR I 248 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TYR I 250 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N GLN E 249 " --> pdb=" O TYR I 250 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP I 252 " --> pdb=" O GLN E 249 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N VAL E 251 " --> pdb=" O ASP I 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 122 through 126 removed outlier: 6.648A pdb=" N ASP C 122 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N TYR G 125 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS C 124 " --> pdb=" O TYR G 125 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP B 122 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N TYR C 125 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS B 124 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 129 through 138 removed outlier: 7.007A pdb=" N SER G 130 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA C 131 " --> pdb=" O SER G 130 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR G 132 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER C 130 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA B 131 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR C 132 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N SER B 130 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 10.146A pdb=" N VAL F 133 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR B 132 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR F 135 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER B 134 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL F 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP B 136 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N SER F 130 " --> pdb=" O ALA J 131 " (cutoff:3.500A) removed outlier: 10.147A pdb=" N VAL J 133 " --> pdb=" O SER F 130 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR F 132 " --> pdb=" O VAL J 133 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR J 135 " --> pdb=" O TYR F 132 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N SER F 134 " --> pdb=" O TYR J 135 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL J 137 " --> pdb=" O SER F 134 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP F 136 " --> pdb=" O VAL J 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 142 through 143 removed outlier: 6.474A pdb=" N ILE B 142 " --> pdb=" O TYR F 143 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE F 142 " --> pdb=" O TYR J 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 146 through 160 removed outlier: 6.817A pdb=" N ILE C 146 " --> pdb=" O THR G 147 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N THR G 149 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN C 148 " --> pdb=" O THR G 149 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASN G 151 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU C 150 " --> pdb=" O ASN G 151 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N THR G 153 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE C 152 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ASN G 155 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN C 154 " --> pdb=" O ASN G 155 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N TYR G 157 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN C 156 " --> pdb=" O TYR G 157 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N SER G 159 " --> pdb=" O ASN C 156 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N TYR C 158 " --> pdb=" O SER G 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 163 through 177 removed outlier: 7.068A pdb=" N ALA C 167 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN G 168 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL C 169 " --> pdb=" O GLN G 168 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN G 170 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE C 171 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER G 172 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS C 173 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR G 174 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 175 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE G 176 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY C 177 " --> pdb=" O ILE G 176 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA B 167 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN C 168 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 169 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN C 170 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE B 171 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER C 172 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS B 173 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR C 174 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B 175 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE C 176 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY B 177 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASN B 164 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA F 167 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR B 166 " --> pdb=" O ALA F 167 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL F 169 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLN B 168 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N PHE F 171 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N GLN B 170 " --> pdb=" O PHE F 171 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N LYS F 173 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N SER B 172 " --> pdb=" O LYS F 173 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL F 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N THR B 174 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N GLY F 177 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ILE B 176 " --> pdb=" O GLY F 177 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASN F 164 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA J 167 " --> pdb=" O ASN F 164 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR F 166 " --> pdb=" O ALA J 167 " (cutoff:3.500A) removed outlier: 10.513A pdb=" N VAL J 169 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLN F 168 " --> pdb=" O VAL J 169 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N PHE J 171 " --> pdb=" O GLN F 168 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N GLN F 170 " --> pdb=" O PHE J 171 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N LYS J 173 " --> pdb=" O GLN F 170 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N SER F 172 " --> pdb=" O LYS J 173 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL J 175 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N THR F 174 " --> pdb=" O VAL J 175 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N GLY J 177 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ILE F 176 " --> pdb=" O GLY J 177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 180 through 187 removed outlier: 9.107A pdb=" N ARG C 180 " --> pdb=" O LEU G 181 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N ASN G 183 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN C 182 " --> pdb=" O ASN G 183 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N THR G 185 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE C 184 " --> pdb=" O THR G 185 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE G 187 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE C 186 " --> pdb=" O ILE G 187 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N ARG B 180 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N ASN C 183 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN B 182 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N THR C 185 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 184 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE C 187 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE B 186 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU B 181 " --> pdb=" O ARG F 180 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN F 182 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN B 183 " --> pdb=" O ASN F 182 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU F 181 " --> pdb=" O ARG J 180 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN J 182 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN F 183 " --> pdb=" O ASN J 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 194 through 198 removed outlier: 6.721A pdb=" N ILE C 195 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR G 198 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR C 197 " --> pdb=" O THR G 198 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 195 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N THR C 198 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR B 197 " --> pdb=" O THR C 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 201 through 203 removed outlier: 6.403A pdb=" N VAL B 202 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL F 202 " --> pdb=" O ILE J 203 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 209 through 230 removed outlier: 6.881A pdb=" N MET C 210 " --> pdb=" O TYR G 211 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N PHE G 213 " --> pdb=" O MET C 210 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP C 212 " --> pdb=" O PHE G 213 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N THR G 215 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N CYS C 214 " --> pdb=" O THR G 215 " (cutoff:3.500A) removed outlier: 10.806A pdb=" N ILE G 217 " --> pdb=" O CYS C 214 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N LEU C 216 " --> pdb=" O ILE G 217 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N ILE G 219 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER C 218 " --> pdb=" O ILE G 219 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N VAL G 221 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS C 220 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ASN G 223 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N HIS C 222 " --> pdb=" O ASN G 223 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL G 225 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ILE C 224 " --> pdb=" O VAL G 225 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N MET G 227 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N LEU C 226 " --> pdb=" O MET G 227 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N GLN G 229 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N MET C 228 " --> pdb=" O GLN G 229 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N MET B 210 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N PHE C 213 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP B 212 " --> pdb=" O PHE C 213 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N THR C 215 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N CYS B 214 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 10.806A pdb=" N ILE C 217 " --> pdb=" O CYS B 214 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N LEU B 216 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N ILE C 219 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER B 218 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N VAL C 221 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS B 220 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ASN C 223 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N HIS B 222 " --> pdb=" O ASN C 223 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 225 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N ILE B 224 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N MET C 227 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N LEU B 226 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N GLN C 229 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N MET B 228 " --> pdb=" O GLN C 229 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR B 215 " --> pdb=" O CYS F 214 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU F 216 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE B 217 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER F 218 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 219 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE F 224 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL B 225 " --> pdb=" O ILE F 224 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU F 226 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N MET B 227 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N MET F 228 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR F 215 " --> pdb=" O CYS J 214 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU J 216 " --> pdb=" O THR F 215 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE F 217 " --> pdb=" O LEU J 216 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER J 218 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE F 219 " --> pdb=" O SER J 218 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE J 224 " --> pdb=" O ASN F 223 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL F 225 " --> pdb=" O ILE J 224 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU J 226 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N MET F 227 " --> pdb=" O LEU J 226 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N MET J 228 " --> pdb=" O MET F 227 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 233 through 253 removed outlier: 6.716A pdb=" N THR C 233 " --> pdb=" O THR G 234 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N TYR G 236 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR C 235 " --> pdb=" O TYR G 236 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N GLY G 238 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE C 237 " --> pdb=" O GLY G 238 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N SER G 240 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS C 239 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N GLN G 242 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU C 241 " --> pdb=" O GLN G 242 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N SER G 244 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 243 " --> pdb=" O SER G 244 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLU G 246 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN C 245 " --> pdb=" O GLU G 246 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N TYR G 248 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG C 247 " --> pdb=" O TYR G 248 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TYR G 250 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N GLN C 249 " --> pdb=" O TYR G 250 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP G 252 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N VAL C 251 " --> pdb=" O ASP G 252 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR B 233 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N TYR C 236 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR B 235 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N GLY C 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE B 237 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N SER C 240 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N HIS B 239 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N GLN C 242 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU B 241 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N SER C 244 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 243 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLU C 246 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN B 245 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TYR C 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG B 247 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TYR C 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N GLN B 249 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP C 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N VAL B 251 " --> pdb=" O ASP C 252 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL F 251 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP B 252 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS F 253 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL J 251 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP F 252 " --> pdb=" O VAL J 251 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS J 253 " --> pdb=" O ASP F 252 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 834 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: 2.99 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3500 1.34 - 1.46: 2675 1.46 - 1.58: 5305 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 11600 Sorted by residual: bond pdb=" N VAL D 123 " pdb=" CA VAL D 123 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.29e-02 6.01e+03 9.22e+00 bond pdb=" N VAL J 123 " pdb=" CA VAL J 123 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.29e-02 6.01e+03 9.17e+00 bond pdb=" N VAL B 123 " pdb=" CA VAL B 123 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.29e-02 6.01e+03 9.05e+00 bond pdb=" N VAL G 123 " pdb=" CA VAL G 123 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.29e-02 6.01e+03 9.04e+00 bond pdb=" N VAL H 123 " pdb=" CA VAL H 123 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.29e-02 6.01e+03 8.98e+00 ... (remaining 11595 not shown) Histogram of bond angle deviations from ideal: 100.66 - 106.78: 220 106.78 - 112.90: 6484 112.90 - 119.01: 2978 119.01 - 125.13: 6028 125.13 - 131.25: 60 Bond angle restraints: 15770 Sorted by residual: angle pdb=" N LYS B 124 " pdb=" CA LYS B 124 " pdb=" C LYS B 124 " ideal model delta sigma weight residual 108.69 118.57 -9.88 1.77e+00 3.19e-01 3.12e+01 angle pdb=" N LYS G 124 " pdb=" CA LYS G 124 " pdb=" C LYS G 124 " ideal model delta sigma weight residual 108.69 118.57 -9.88 1.77e+00 3.19e-01 3.11e+01 angle pdb=" N LYS D 124 " pdb=" CA LYS D 124 " pdb=" C LYS D 124 " ideal model delta sigma weight residual 108.69 118.56 -9.87 1.77e+00 3.19e-01 3.11e+01 angle pdb=" N LYS C 124 " pdb=" CA LYS C 124 " pdb=" C LYS C 124 " ideal model delta sigma weight residual 108.69 118.54 -9.85 1.77e+00 3.19e-01 3.10e+01 angle pdb=" N LYS J 124 " pdb=" CA LYS J 124 " pdb=" C LYS J 124 " ideal model delta sigma weight residual 108.69 118.53 -9.84 1.77e+00 3.19e-01 3.09e+01 ... (remaining 15765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 6660 14.82 - 29.64: 620 29.64 - 44.46: 120 44.46 - 59.28: 80 59.28 - 74.10: 10 Dihedral angle restraints: 7490 sinusoidal: 3430 harmonic: 4060 Sorted by residual: dihedral pdb=" CA LYS D 139 " pdb=" C LYS D 139 " pdb=" N ARG D 140 " pdb=" CA ARG D 140 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA LYS E 139 " pdb=" C LYS E 139 " pdb=" N ARG E 140 " pdb=" CA ARG E 140 " ideal model delta harmonic sigma weight residual 180.00 162.80 17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA LYS I 139 " pdb=" C LYS I 139 " pdb=" N ARG I 140 " pdb=" CA ARG I 140 " ideal model delta harmonic sigma weight residual 180.00 162.80 17.20 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 7487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1514 0.071 - 0.142: 436 0.142 - 0.213: 40 0.213 - 0.284: 0 0.284 - 0.355: 20 Chirality restraints: 2010 Sorted by residual: chirality pdb=" C1 NAG F 304 " pdb=" ND2 ASN F 145 " pdb=" C2 NAG F 304 " pdb=" O5 NAG F 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C1 NAG G 304 " pdb=" ND2 ASN G 145 " pdb=" C2 NAG G 304 " pdb=" O5 NAG G 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C1 NAG E 304 " pdb=" ND2 ASN E 145 " pdb=" C2 NAG E 304 " pdb=" O5 NAG E 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 2007 not shown) Planarity restraints: 1940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN E 138 " 0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C GLN E 138 " -0.068 2.00e-02 2.50e+03 pdb=" O GLN E 138 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS E 139 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 138 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C GLN C 138 " 0.067 2.00e-02 2.50e+03 pdb=" O GLN C 138 " -0.026 2.00e-02 2.50e+03 pdb=" N LYS C 139 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN I 138 " 0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C GLN I 138 " -0.067 2.00e-02 2.50e+03 pdb=" O GLN I 138 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS I 139 " 0.023 2.00e-02 2.50e+03 ... (remaining 1937 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 209 2.71 - 3.26: 10828 3.26 - 3.81: 17579 3.81 - 4.35: 22389 4.35 - 4.90: 35509 Nonbonded interactions: 86514 Sorted by model distance: nonbonded pdb=" OG1 THR F 231 " pdb=" OG1 THR F 234 " model vdw 2.166 2.440 nonbonded pdb=" OG1 THR I 231 " pdb=" OG1 THR I 234 " model vdw 2.166 2.440 nonbonded pdb=" OG1 THR B 231 " pdb=" OG1 THR B 234 " model vdw 2.166 2.440 nonbonded pdb=" OG1 THR A 231 " pdb=" OG1 THR A 234 " model vdw 2.166 2.440 nonbonded pdb=" OG1 THR J 231 " pdb=" OG1 THR J 234 " model vdw 2.167 2.440 ... (remaining 86509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.320 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.990 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 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 : 0.005 0.041 11600 Z= 0.317 Angle : 0.870 9.879 15770 Z= 0.499 Chirality : 0.070 0.355 2010 Planarity : 0.006 0.039 1900 Dihedral : 13.331 74.103 4860 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 239 PHE 0.011 0.003 PHE F 171 TYR 0.028 0.003 TYR B 157 ARG 0.001 0.000 ARG G 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.293 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1775 time to fit residues: 37.6054 Evaluate side-chains 110 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 239 HIS B 138 GLN B 239 HIS D 138 GLN D 242 GLN E 138 GLN F 138 GLN G 138 GLN H 138 GLN I 138 GLN J 138 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11600 Z= 0.276 Angle : 0.765 7.812 15770 Z= 0.418 Chirality : 0.063 0.366 2010 Planarity : 0.003 0.019 1900 Dihedral : 9.819 56.673 2330 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 3.81 % Allowed : 11.67 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 239 PHE 0.022 0.004 PHE C 213 TYR 0.026 0.003 TYR H 248 ARG 0.002 0.000 ARG F 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 123 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: F 135 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.6619 (m-80) REVERT: H 216 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7808 (pp) outliers start: 48 outliers final: 25 residues processed: 153 average time/residue: 0.1816 time to fit residues: 43.4352 Evaluate side-chains 140 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 135 TYR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 chunk 94 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN E 138 GLN H 138 GLN I 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11600 Z= 0.328 Angle : 0.785 7.673 15770 Z= 0.430 Chirality : 0.062 0.358 2010 Planarity : 0.004 0.025 1900 Dihedral : 10.163 57.782 2330 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 6.51 % Allowed : 14.76 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 239 PHE 0.019 0.004 PHE B 213 TYR 0.032 0.003 TYR H 248 ARG 0.001 0.000 ARG E 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 127 time to evaluate : 1.249 Fit side-chains REVERT: A 135 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.5200 (m-80) REVERT: C 135 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.5773 (m-80) REVERT: C 191 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6435 (t0) REVERT: D 227 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6714 (mtp) REVERT: D 242 GLN cc_start: 0.7110 (mt0) cc_final: 0.6906 (mt0) REVERT: F 135 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.6805 (m-80) REVERT: H 135 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.5343 (m-80) REVERT: H 216 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7794 (pp) REVERT: I 135 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6270 (m-80) REVERT: J 191 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.5998 (t0) outliers start: 82 outliers final: 47 residues processed: 176 average time/residue: 0.1777 time to fit residues: 49.1058 Evaluate side-chains 179 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 123 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 135 TYR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 182 ASN Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN B 138 GLN D 138 GLN D 242 GLN J 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11600 Z= 0.272 Angle : 0.738 7.394 15770 Z= 0.404 Chirality : 0.061 0.424 2010 Planarity : 0.003 0.022 1900 Dihedral : 9.712 57.439 2330 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 8.17 % Allowed : 13.49 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 239 PHE 0.016 0.003 PHE B 213 TYR 0.028 0.003 TYR H 248 ARG 0.001 0.000 ARG J 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 125 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.5067 (m-80) REVERT: A 145 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7668 (t0) REVERT: B 135 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.6537 (m-80) REVERT: B 145 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7845 (t0) REVERT: C 135 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.5622 (m-80) REVERT: C 145 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7614 (t0) REVERT: D 227 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6778 (mtp) REVERT: E 145 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7732 (t0) REVERT: E 178 LYS cc_start: 0.7352 (mttt) cc_final: 0.6318 (tptp) REVERT: F 145 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7769 (t0) REVERT: H 135 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.5362 (m-80) REVERT: H 145 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7388 (t0) REVERT: H 216 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7815 (pp) REVERT: I 135 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6128 (m-80) REVERT: I 145 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7182 (t0) REVERT: J 191 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.5995 (t0) outliers start: 103 outliers final: 64 residues processed: 191 average time/residue: 0.1767 time to fit residues: 52.9221 Evaluate side-chains 201 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 122 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 207 MET Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 182 ASN Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 1 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 107 optimal weight: 30.0000 chunk 86 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 31 optimal weight: 40.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11600 Z= 0.375 Angle : 0.837 7.844 15770 Z= 0.459 Chirality : 0.063 0.410 2010 Planarity : 0.004 0.026 1900 Dihedral : 10.278 59.851 2330 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 8.02 % Allowed : 13.73 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS F 239 PHE 0.017 0.004 PHE D 213 TYR 0.037 0.004 TYR H 248 ARG 0.001 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 132 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 135 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.5475 (m-80) REVERT: A 145 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7339 (t0) REVERT: B 145 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.7652 (t0) REVERT: C 135 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.5581 (m-80) REVERT: C 145 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7594 (t0) REVERT: C 150 LEU cc_start: 0.8509 (mp) cc_final: 0.8181 (mp) REVERT: C 178 LYS cc_start: 0.7738 (mttt) cc_final: 0.6753 (tptp) REVERT: C 211 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.5337 (m-10) REVERT: D 227 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6998 (mtp) REVERT: E 178 LYS cc_start: 0.7192 (mttt) cc_final: 0.6460 (tptp) REVERT: F 135 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.6637 (m-80) REVERT: F 145 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7618 (t0) REVERT: F 178 LYS cc_start: 0.7782 (mttt) cc_final: 0.6862 (tptp) REVERT: F 211 TYR cc_start: 0.6669 (OUTLIER) cc_final: 0.5747 (m-10) REVERT: G 145 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.7222 (t0) REVERT: H 135 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.5583 (m-80) REVERT: H 145 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7301 (t0) REVERT: H 178 LYS cc_start: 0.7798 (mttt) cc_final: 0.6793 (tptp) REVERT: H 211 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6282 (m-80) REVERT: H 216 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7862 (pp) REVERT: I 135 TYR cc_start: 0.7196 (OUTLIER) cc_final: 0.6339 (m-80) REVERT: I 145 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7047 (t0) REVERT: J 135 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6509 (m-80) REVERT: J 145 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7316 (t0) outliers start: 101 outliers final: 71 residues processed: 200 average time/residue: 0.1775 time to fit residues: 55.1752 Evaluate side-chains 211 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 121 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 135 TYR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 211 TYR Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 182 ASN Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 135 TYR Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 73 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 40.0000 chunk 10 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 66 optimal weight: 40.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN B 170 GLN ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11600 Z= 0.303 Angle : 0.775 7.632 15770 Z= 0.425 Chirality : 0.062 0.475 2010 Planarity : 0.004 0.028 1900 Dihedral : 9.940 59.966 2330 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 8.81 % Allowed : 13.33 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 239 PHE 0.016 0.003 PHE I 213 TYR 0.029 0.003 TYR H 248 ARG 0.001 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 140 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 135 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.5181 (m-80) REVERT: A 145 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7497 (t0) REVERT: A 150 LEU cc_start: 0.8362 (mp) cc_final: 0.8111 (mp) REVERT: B 135 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6345 (m-80) REVERT: B 145 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7519 (t0) REVERT: B 178 LYS cc_start: 0.7737 (mttt) cc_final: 0.6464 (tptp) REVERT: B 216 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8081 (pp) REVERT: C 135 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.5282 (m-80) REVERT: C 145 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7374 (t0) REVERT: C 150 LEU cc_start: 0.8484 (mp) cc_final: 0.8281 (mp) REVERT: C 178 LYS cc_start: 0.7730 (mttt) cc_final: 0.6689 (tptp) REVERT: C 211 TYR cc_start: 0.6888 (OUTLIER) cc_final: 0.5330 (m-10) REVERT: D 227 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.7173 (mtp) REVERT: E 145 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7513 (t0) REVERT: E 175 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7746 (t) REVERT: E 178 LYS cc_start: 0.7163 (mttt) cc_final: 0.6452 (tptp) REVERT: E 211 TYR cc_start: 0.6619 (OUTLIER) cc_final: 0.6386 (m-10) REVERT: F 135 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6711 (m-80) REVERT: F 145 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7677 (t0) REVERT: F 178 LYS cc_start: 0.7785 (mttt) cc_final: 0.6774 (tptp) REVERT: F 211 TYR cc_start: 0.6747 (OUTLIER) cc_final: 0.5882 (m-10) REVERT: H 135 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.5552 (m-80) REVERT: H 145 ASN cc_start: 0.7952 (OUTLIER) cc_final: 0.7431 (t0) REVERT: H 150 LEU cc_start: 0.8507 (mp) cc_final: 0.8225 (mp) REVERT: H 178 LYS cc_start: 0.7775 (mttt) cc_final: 0.6823 (tptp) REVERT: H 211 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6254 (m-10) REVERT: H 216 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7872 (pp) REVERT: I 135 TYR cc_start: 0.7135 (OUTLIER) cc_final: 0.6294 (m-80) REVERT: I 145 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7130 (t0) REVERT: J 135 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.6385 (m-80) REVERT: J 145 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7283 (t0) REVERT: J 178 LYS cc_start: 0.7449 (mttt) cc_final: 0.6481 (tptp) outliers start: 111 outliers final: 78 residues processed: 212 average time/residue: 0.1992 time to fit residues: 64.6579 Evaluate side-chains 239 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 138 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 211 TYR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 211 TYR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 135 TYR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 207 MET Chi-restraints excluded: chain G residue 211 TYR Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 211 TYR Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 182 ASN Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 135 TYR Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.3980 chunk 14 optimal weight: 30.0000 chunk 71 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 57 optimal weight: 30.0000 chunk 77 optimal weight: 7.9990 overall best weight: 6.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN H 170 GLN J 138 GLN J 170 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11600 Z= 0.248 Angle : 0.728 7.381 15770 Z= 0.397 Chirality : 0.060 0.440 2010 Planarity : 0.003 0.025 1900 Dihedral : 9.533 59.676 2330 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 8.17 % Allowed : 13.81 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 239 PHE 0.014 0.003 PHE B 237 TYR 0.024 0.003 TYR H 248 ARG 0.001 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 137 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.4865 (m-80) REVERT: A 145 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7525 (t0) REVERT: A 150 LEU cc_start: 0.8314 (mp) cc_final: 0.8072 (mp) REVERT: B 145 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7585 (t0) REVERT: B 178 LYS cc_start: 0.7723 (mttt) cc_final: 0.6450 (tptp) REVERT: B 216 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8057 (pp) REVERT: C 135 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.5575 (m-80) REVERT: C 145 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7479 (t0) REVERT: C 178 LYS cc_start: 0.7800 (mttt) cc_final: 0.6682 (tptp) REVERT: D 227 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6982 (mtp) REVERT: E 145 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7679 (t0) REVERT: E 178 LYS cc_start: 0.7207 (mttt) cc_final: 0.6481 (tptp) REVERT: F 135 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.6908 (m-80) REVERT: F 145 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7826 (t0) REVERT: F 178 LYS cc_start: 0.7738 (mttt) cc_final: 0.6733 (tptp) REVERT: H 135 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.5619 (m-80) REVERT: H 145 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7441 (t0) REVERT: H 178 LYS cc_start: 0.7743 (mttt) cc_final: 0.6835 (tptp) REVERT: H 216 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7795 (pp) REVERT: I 145 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7259 (t0) REVERT: J 145 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7419 (t0) REVERT: J 178 LYS cc_start: 0.7508 (mttt) cc_final: 0.6506 (tptp) outliers start: 103 outliers final: 75 residues processed: 201 average time/residue: 0.1954 time to fit residues: 60.9772 Evaluate side-chains 222 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 132 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 135 TYR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 207 MET Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain I residue 120 SER Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 182 ASN Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN J 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11600 Z= 0.247 Angle : 0.730 7.436 15770 Z= 0.397 Chirality : 0.060 0.442 2010 Planarity : 0.003 0.027 1900 Dihedral : 9.349 58.488 2330 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 7.62 % Allowed : 14.76 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 239 PHE 0.016 0.003 PHE B 237 TYR 0.022 0.003 TYR H 248 ARG 0.001 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 132 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 135 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.4808 (m-80) REVERT: A 145 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7407 (t0) REVERT: B 145 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7495 (t0) REVERT: B 178 LYS cc_start: 0.7690 (mttt) cc_final: 0.6459 (tptp) REVERT: B 216 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8052 (pp) REVERT: C 135 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.5357 (m-80) REVERT: C 145 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7452 (t0) REVERT: C 178 LYS cc_start: 0.7785 (mttt) cc_final: 0.6682 (tptp) REVERT: D 227 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6989 (mtp) REVERT: E 145 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7451 (t0) REVERT: E 178 LYS cc_start: 0.7187 (mttt) cc_final: 0.6481 (tptp) REVERT: F 135 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: F 145 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7596 (t0) REVERT: F 178 LYS cc_start: 0.7579 (mttt) cc_final: 0.6800 (tptp) REVERT: H 135 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.5320 (m-80) REVERT: H 145 ASN cc_start: 0.7842 (OUTLIER) cc_final: 0.7167 (t0) REVERT: H 178 LYS cc_start: 0.7769 (mttt) cc_final: 0.6880 (tptp) REVERT: H 216 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7760 (pp) REVERT: H 228 MET cc_start: 0.8034 (tpp) cc_final: 0.7765 (tpp) REVERT: I 145 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.7035 (t0) REVERT: J 145 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.7260 (t0) REVERT: J 178 LYS cc_start: 0.7517 (mttt) cc_final: 0.6527 (tptp) outliers start: 96 outliers final: 75 residues processed: 189 average time/residue: 0.1806 time to fit residues: 52.5441 Evaluate side-chains 222 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 132 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 135 TYR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 207 MET Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain I residue 120 SER Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 182 ASN Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 105 optimal weight: 30.0000 chunk 110 optimal weight: 40.0000 chunk 76 optimal weight: 30.0000 chunk 123 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11600 Z= 0.240 Angle : 0.721 7.413 15770 Z= 0.391 Chirality : 0.060 0.422 2010 Planarity : 0.003 0.026 1900 Dihedral : 9.196 59.161 2330 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 7.30 % Allowed : 14.92 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 239 PHE 0.016 0.003 PHE B 237 TYR 0.022 0.003 TYR H 248 ARG 0.001 0.000 ARG J 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 135 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 135 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.4806 (m-80) REVERT: A 145 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7398 (t0) REVERT: B 145 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7502 (t0) REVERT: B 178 LYS cc_start: 0.7454 (mttt) cc_final: 0.6506 (tptp) REVERT: B 216 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8050 (pp) REVERT: C 135 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.5392 (m-80) REVERT: C 145 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7514 (t0) REVERT: C 178 LYS cc_start: 0.7774 (mttt) cc_final: 0.6639 (tptp) REVERT: D 227 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.7029 (mtp) REVERT: E 145 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7512 (t0) REVERT: E 178 LYS cc_start: 0.7163 (mttt) cc_final: 0.6480 (tptp) REVERT: F 145 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7609 (t0) REVERT: F 178 LYS cc_start: 0.7573 (mttt) cc_final: 0.6803 (tptp) REVERT: G 145 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7051 (t0) REVERT: G 178 LYS cc_start: 0.7642 (mttt) cc_final: 0.6323 (tptp) REVERT: H 135 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.5337 (m-80) REVERT: H 145 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7324 (t0) REVERT: H 178 LYS cc_start: 0.7740 (mttt) cc_final: 0.6864 (tptp) REVERT: H 216 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7753 (pp) REVERT: H 228 MET cc_start: 0.8058 (tpp) cc_final: 0.7764 (tpp) REVERT: I 145 ASN cc_start: 0.7868 (OUTLIER) cc_final: 0.7068 (t0) REVERT: J 145 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7316 (t0) REVERT: J 178 LYS cc_start: 0.7527 (mttt) cc_final: 0.6551 (tptp) outliers start: 92 outliers final: 74 residues processed: 187 average time/residue: 0.1845 time to fit residues: 52.8456 Evaluate side-chains 222 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 133 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 207 MET Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain I residue 120 SER Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 182 ASN Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 79 optimal weight: 30.0000 chunk 63 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN B 138 GLN ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN J 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11600 Z= 0.312 Angle : 0.783 7.671 15770 Z= 0.428 Chirality : 0.062 0.440 2010 Planarity : 0.004 0.027 1900 Dihedral : 9.540 59.898 2330 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 7.46 % Allowed : 14.92 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 239 PHE 0.016 0.003 PHE I 213 TYR 0.028 0.003 TYR H 248 ARG 0.003 0.000 ARG J 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 141 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: A 135 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.5186 (m-80) REVERT: A 145 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7508 (t0) REVERT: B 145 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7546 (t0) REVERT: B 178 LYS cc_start: 0.7431 (mttt) cc_final: 0.6504 (tptp) REVERT: B 216 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8076 (pp) REVERT: C 135 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.5418 (m-80) REVERT: C 145 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7532 (t0) REVERT: C 178 LYS cc_start: 0.7557 (mttt) cc_final: 0.6695 (tptp) REVERT: E 145 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7549 (t0) REVERT: E 178 LYS cc_start: 0.7216 (mttt) cc_final: 0.6518 (tptp) REVERT: F 135 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.6920 (m-80) REVERT: F 145 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7629 (t0) REVERT: F 178 LYS cc_start: 0.7712 (mttt) cc_final: 0.6942 (tptp) REVERT: G 145 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7122 (t0) REVERT: G 178 LYS cc_start: 0.7696 (mttt) cc_final: 0.6462 (tptp) REVERT: H 135 TYR cc_start: 0.7367 (OUTLIER) cc_final: 0.5622 (m-80) REVERT: H 145 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7203 (t0) REVERT: H 178 LYS cc_start: 0.7516 (mttt) cc_final: 0.6912 (tptp) REVERT: H 211 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6307 (m-10) REVERT: H 216 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7798 (pp) REVERT: H 228 MET cc_start: 0.8003 (tpp) cc_final: 0.7711 (tpp) REVERT: I 145 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7075 (t0) REVERT: J 145 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7331 (t0) REVERT: J 178 LYS cc_start: 0.7566 (mttt) cc_final: 0.6626 (tptp) outliers start: 94 outliers final: 77 residues processed: 193 average time/residue: 0.1978 time to fit residues: 57.6995 Evaluate side-chains 231 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 138 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain F residue 135 TYR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 211 TYR Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain I residue 120 SER Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 182 ASN Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 90 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN G 170 GLN I 170 GLN J 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5544 r_free = 0.5544 target = 0.420258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5677 r_free = 0.5677 target = 0.351311 restraints weight = 12852.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.5715 r_free = 0.5715 target = 0.349686 restraints weight = 21398.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.5740 r_free = 0.5740 target = 0.346807 restraints weight = 18121.273| |-----------------------------------------------------------------------------| r_work (final): 0.5489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11600 Z= 0.281 Angle : 0.752 7.613 15770 Z= 0.410 Chirality : 0.061 0.432 2010 Planarity : 0.004 0.026 1900 Dihedral : 9.454 59.844 2330 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer: Outliers : 7.30 % Allowed : 15.24 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 239 PHE 0.015 0.003 PHE B 237 TYR 0.025 0.003 TYR H 248 ARG 0.001 0.000 ARG J 140 =============================================================================== Job complete usr+sys time: 1944.90 seconds wall clock time: 36 minutes 38.84 seconds (2198.84 seconds total)