Starting phenix.real_space_refine on Tue Apr 9 00:50:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbo_27293/04_2024/8dbo_27293_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbo_27293/04_2024/8dbo_27293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbo_27293/04_2024/8dbo_27293.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbo_27293/04_2024/8dbo_27293.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbo_27293/04_2024/8dbo_27293_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbo_27293/04_2024/8dbo_27293_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.347 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: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 12 5.21 5 S 102 5.16 5 C 9210 2.51 5 N 2628 2.21 5 O 2898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E ARG 196": "NH1" <-> "NH2" Residue "E GLU 201": "OE1" <-> "OE2" Residue "E TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F ARG 196": "NH1" <-> "NH2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14880 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2416 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "B" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2416 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "C" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2416 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "D" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2416 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "E" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2416 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "F" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2416 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 7.43, per 1000 atoms: 0.50 Number of scatterers: 14880 At special positions: 0 Unit cell: (120.35, 126.99, 75.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 30 15.00 Mg 12 11.99 O 2898 8.00 N 2628 7.00 C 9210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.33 Conformation dependent library (CDL) restraints added in 3.0 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 18 sheets defined 36.7% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 255 through 262 removed outlier: 4.554A pdb=" N ILE A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.708A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 310 through 313 Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 63 through 79 Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS B 176 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 255 through 262 removed outlier: 4.554A pdb=" N ILE B 258 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.708A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 305 Processing helix chain 'B' and resid 310 through 313 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 108 through 119 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 255 through 262 removed outlier: 4.555A pdb=" N ILE C 258 " --> pdb=" O GLY C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.708A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 305 Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 63 through 79 Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 148 through 158 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 255 through 262 removed outlier: 4.554A pdb=" N ILE D 258 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 283 removed outlier: 3.708A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 310 through 313 Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 148 through 158 Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS E 176 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 255 through 262 removed outlier: 4.554A pdb=" N ILE E 258 " --> pdb=" O GLY E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.708A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 305 Processing helix chain 'E' and resid 310 through 313 Processing helix chain 'F' and resid 13 through 22 Processing helix chain 'F' and resid 63 through 79 Processing helix chain 'F' and resid 108 through 119 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'F' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS F 176 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 255 through 262 removed outlier: 4.554A pdb=" N ILE F 258 " --> pdb=" O GLY F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 283 removed outlier: 3.707A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 305 Processing helix chain 'F' and resid 310 through 313 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP A 52 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE A 7 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR A 54 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG A 84 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE A 55 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR A 86 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS A 123 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE A 89 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 125 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR A 126 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP A 143 " --> pdb=" O THR A 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 30 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 287 through 290 removed outlier: 7.886A pdb=" N GLN A 288 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 269 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE A 290 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 271 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL A 244 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 269 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 246 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL A 271 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU A 248 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA A 216 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 218 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR A 166 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL A 219 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A 168 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER A 169 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA A 190 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP B 52 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE B 7 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR B 54 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG B 84 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE B 55 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR B 86 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS B 123 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE B 89 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE B 125 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N THR B 126 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP B 143 " --> pdb=" O THR B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 30 through 34 Processing sheet with id= F, first strand: chain 'B' and resid 287 through 290 removed outlier: 7.886A pdb=" N GLN B 288 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 269 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE B 290 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 271 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL B 244 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 269 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA B 246 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL B 271 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 248 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA B 216 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU B 218 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR B 166 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL B 219 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL B 168 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP B 188 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER B 169 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA B 190 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP C 52 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE C 7 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR C 54 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG C 84 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE C 55 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR C 86 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS C 123 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE C 89 " --> pdb=" O HIS C 123 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE C 125 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR C 126 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASP C 143 " --> pdb=" O THR C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 30 through 34 Processing sheet with id= I, first strand: chain 'C' and resid 287 through 290 removed outlier: 7.886A pdb=" N GLN C 288 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL C 269 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE C 290 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL C 271 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL C 244 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL C 269 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA C 246 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL C 271 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU C 248 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA C 216 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE C 247 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU C 218 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR C 166 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL C 219 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL C 168 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP C 188 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER C 169 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA C 190 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP D 52 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE D 7 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR D 54 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG D 84 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE D 55 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR D 86 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS D 123 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE D 89 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE D 125 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR D 126 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASP D 143 " --> pdb=" O THR D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 30 through 34 Processing sheet with id= L, first strand: chain 'D' and resid 287 through 290 removed outlier: 7.885A pdb=" N GLN D 288 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL D 269 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE D 290 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 271 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL D 244 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL D 269 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA D 246 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL D 271 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU D 248 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA D 216 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE D 247 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU D 218 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR D 166 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL D 219 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL D 168 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP D 188 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER D 169 " --> pdb=" O ASP D 188 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA D 190 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP E 52 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE E 7 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR E 54 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG E 84 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE E 55 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR E 86 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS E 123 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE E 89 " --> pdb=" O HIS E 123 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE E 125 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR E 126 " --> pdb=" O PRO E 141 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP E 143 " --> pdb=" O THR E 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 30 through 34 Processing sheet with id= O, first strand: chain 'E' and resid 287 through 290 removed outlier: 7.886A pdb=" N GLN E 288 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL E 269 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE E 290 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL E 271 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL E 244 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 269 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA E 246 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL E 271 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU E 248 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA E 216 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE E 247 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU E 218 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR E 166 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL E 219 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL E 168 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP E 188 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N SER E 169 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA E 190 " --> pdb=" O SER E 169 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP F 52 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE F 7 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR F 54 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG F 84 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE F 55 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR F 86 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS F 123 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE F 89 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE F 125 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N THR F 126 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASP F 143 " --> pdb=" O THR F 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 30 through 34 Processing sheet with id= R, first strand: chain 'F' and resid 287 through 290 removed outlier: 7.885A pdb=" N GLN F 288 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL F 269 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE F 290 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL F 271 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL F 244 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL F 269 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA F 246 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N VAL F 271 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU F 248 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA F 216 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE F 247 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU F 218 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR F 166 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL F 219 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL F 168 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER F 169 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA F 190 " --> pdb=" O SER F 169 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.36 Time building geometry restraints manager: 6.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4953 1.34 - 1.46: 1956 1.46 - 1.57: 7989 1.57 - 1.69: 36 1.69 - 1.81: 150 Bond restraints: 15084 Sorted by residual: bond pdb=" C4 ADP A 405 " pdb=" C5 ADP A 405 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C4 ADP B 405 " pdb=" C5 ADP B 405 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 15079 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.98: 345 105.98 - 113.32: 8830 113.32 - 120.66: 6205 120.66 - 128.01: 4954 128.01 - 135.35: 138 Bond angle restraints: 20472 Sorted by residual: angle pdb=" PA ADP F 403 " pdb=" O3A ADP F 403 " pdb=" PB ADP F 403 " ideal model delta sigma weight residual 120.50 135.35 -14.85 3.00e+00 1.11e-01 2.45e+01 angle pdb=" PA ADP E 403 " pdb=" O3A ADP E 403 " pdb=" PB ADP E 403 " ideal model delta sigma weight residual 120.50 135.35 -14.85 3.00e+00 1.11e-01 2.45e+01 angle pdb=" PA ADP C 403 " pdb=" O3A ADP C 403 " pdb=" PB ADP C 403 " ideal model delta sigma weight residual 120.50 135.34 -14.84 3.00e+00 1.11e-01 2.45e+01 angle pdb=" PA ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PB ADP B 402 " ideal model delta sigma weight residual 120.50 135.32 -14.82 3.00e+00 1.11e-01 2.44e+01 angle pdb=" PA ADP D 402 " pdb=" O3A ADP D 402 " pdb=" PB ADP D 402 " ideal model delta sigma weight residual 120.50 135.31 -14.81 3.00e+00 1.11e-01 2.44e+01 ... (remaining 20467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 8826 34.00 - 67.99: 297 67.99 - 101.99: 33 101.99 - 135.99: 15 135.99 - 169.99: 9 Dihedral angle restraints: 9180 sinusoidal: 3672 harmonic: 5508 Sorted by residual: dihedral pdb=" O2A ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PA ADP B 402 " pdb=" PB ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 109.99 -169.99 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP D 402 " pdb=" O3A ADP D 402 " pdb=" PA ADP D 402 " pdb=" PB ADP D 402 " ideal model delta sinusoidal sigma weight residual -60.00 109.97 -169.97 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP F 403 " pdb=" O3A ADP F 403 " pdb=" PA ADP F 403 " pdb=" PB ADP F 403 " ideal model delta sinusoidal sigma weight residual -60.00 109.95 -169.95 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 9177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1508 0.041 - 0.082: 600 0.082 - 0.123: 240 0.123 - 0.163: 46 0.163 - 0.204: 12 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CA VAL C 151 " pdb=" N VAL C 151 " pdb=" C VAL C 151 " pdb=" CB VAL C 151 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL B 151 " pdb=" N VAL B 151 " pdb=" C VAL B 151 " pdb=" CB VAL B 151 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL E 151 " pdb=" N VAL E 151 " pdb=" C VAL E 151 " pdb=" CB VAL E 151 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2403 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 65 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00 pdb=" CG ASP C 65 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP C 65 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP C 65 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP B 402 " 0.019 2.00e-02 2.50e+03 9.40e-03 2.43e+00 pdb=" C2 ADP B 402 " -0.005 2.00e-02 2.50e+03 pdb=" C4 ADP B 402 " -0.002 2.00e-02 2.50e+03 pdb=" C5 ADP B 402 " -0.003 2.00e-02 2.50e+03 pdb=" C6 ADP B 402 " -0.000 2.00e-02 2.50e+03 pdb=" C8 ADP B 402 " -0.009 2.00e-02 2.50e+03 pdb=" N1 ADP B 402 " -0.005 2.00e-02 2.50e+03 pdb=" N3 ADP B 402 " -0.003 2.00e-02 2.50e+03 pdb=" N6 ADP B 402 " 0.019 2.00e-02 2.50e+03 pdb=" N7 ADP B 402 " -0.009 2.00e-02 2.50e+03 pdb=" N9 ADP B 402 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 65 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" CG ASP A 65 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP A 65 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 65 " -0.010 2.00e-02 2.50e+03 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 96 2.47 - 3.08: 10827 3.08 - 3.69: 24270 3.69 - 4.29: 37587 4.29 - 4.90: 59229 Nonbonded interactions: 132009 Sorted by model distance: nonbonded pdb="MG MG B 403 " pdb=" O HOH B 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG F 404 " pdb=" O HOH F 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG A 403 " pdb=" O HOH A 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG E 404 " pdb=" O HOH E 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG D 403 " pdb=" O HOH D 503 " model vdw 1.867 2.170 ... (remaining 132004 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 317 or resid 404)) selection = (chain 'B' and (resid 2 through 317 or resid 404)) selection = (chain 'C' and (resid 2 through 317 or resid 404)) selection = (chain 'D' and (resid 2 through 317 or resid 404)) selection = (chain 'E' and (resid 2 through 317 or resid 404)) selection = (chain 'F' and (resid 2 through 317 or resid 404)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.240 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: 0.000 Extract box with map and model: 6.850 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 41.640 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 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 : 0.007 0.107 15084 Z= 0.468 Angle : 1.022 14.848 20472 Z= 0.449 Chirality : 0.053 0.204 2406 Planarity : 0.003 0.020 2568 Dihedral : 18.642 169.985 5592 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.37 % Allowed : 14.23 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.19), residues: 1884 helix: 1.78 (0.20), residues: 702 sheet: -0.38 (0.24), residues: 450 loop : 0.24 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP E 162 HIS 0.007 0.001 HIS F 12 PHE 0.013 0.002 PHE F 138 TYR 0.011 0.002 TYR E 311 ARG 0.008 0.001 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 555 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.7724 (tt) cc_final: 0.7510 (mm) REVERT: A 280 LYS cc_start: 0.7820 (mmtm) cc_final: 0.7458 (mmmt) REVERT: B 280 LYS cc_start: 0.7870 (mmtm) cc_final: 0.7539 (mmmt) REVERT: C 191 LEU cc_start: 0.7852 (tt) cc_final: 0.7590 (mm) REVERT: C 280 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7680 (mmmt) REVERT: D 191 LEU cc_start: 0.7854 (tt) cc_final: 0.7601 (mm) REVERT: D 280 LYS cc_start: 0.7943 (mmtm) cc_final: 0.7698 (mmmt) REVERT: E 280 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7543 (mmmt) REVERT: F 280 LYS cc_start: 0.7829 (mmtm) cc_final: 0.7464 (mmmt) outliers start: 54 outliers final: 11 residues processed: 591 average time/residue: 1.3561 time to fit residues: 874.1675 Evaluate side-chains 382 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 371 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 196 ARG Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.7980 chunk 140 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 0.0980 chunk 108 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN B 263 ASN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 ASN E 97 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15084 Z= 0.171 Angle : 0.647 7.730 20472 Z= 0.297 Chirality : 0.047 0.154 2406 Planarity : 0.004 0.033 2568 Dihedral : 15.853 157.430 2170 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.87 % Allowed : 22.97 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 1884 helix: 1.54 (0.20), residues: 702 sheet: -0.51 (0.23), residues: 498 loop : 0.02 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 162 HIS 0.004 0.001 HIS F 12 PHE 0.009 0.001 PHE F 138 TYR 0.005 0.001 TYR C 54 ARG 0.004 0.001 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 352 time to evaluate : 1.611 Fit side-chains revert: symmetry clash REVERT: B 97 GLN cc_start: 0.7862 (tp40) cc_final: 0.7660 (tp-100) REVERT: F 288 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.6891 (mt0) outliers start: 62 outliers final: 40 residues processed: 392 average time/residue: 1.1582 time to fit residues: 504.6380 Evaluate side-chains 373 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 332 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 288 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 182 optimal weight: 0.7980 chunk 150 optimal weight: 0.0270 chunk 167 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 283 HIS C 133 GLN C 186 ASN D 186 ASN D 283 HIS E 97 GLN E 133 GLN E 263 ASN E 283 HIS F 186 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15084 Z= 0.187 Angle : 0.646 7.586 20472 Z= 0.295 Chirality : 0.046 0.152 2406 Planarity : 0.003 0.021 2568 Dihedral : 15.565 163.874 2152 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.87 % Allowed : 23.22 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.19), residues: 1884 helix: 1.11 (0.20), residues: 708 sheet: -0.57 (0.23), residues: 498 loop : -0.10 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 162 HIS 0.004 0.001 HIS A 12 PHE 0.010 0.002 PHE B 313 TYR 0.010 0.001 TYR D 54 ARG 0.004 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 339 time to evaluate : 1.720 Fit side-chains REVERT: A 78 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6914 (tptp) REVERT: A 176 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6553 (mptt) REVERT: A 302 ARG cc_start: 0.6787 (mpt180) cc_final: 0.6569 (mpt90) REVERT: C 176 LYS cc_start: 0.6827 (OUTLIER) cc_final: 0.6519 (mttp) REVERT: F 176 LYS cc_start: 0.6832 (OUTLIER) cc_final: 0.6530 (mptt) outliers start: 62 outliers final: 30 residues processed: 374 average time/residue: 1.1444 time to fit residues: 476.4651 Evaluate side-chains 366 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 332 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 133 GLN C 186 ASN C 283 HIS D 186 ASN E 75 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN F 283 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15084 Z= 0.249 Angle : 0.690 7.900 20472 Z= 0.319 Chirality : 0.048 0.161 2406 Planarity : 0.004 0.026 2568 Dihedral : 15.287 155.565 2152 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.18 % Allowed : 23.03 % Favored : 72.78 % 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: -0.56 (0.18), residues: 1884 helix: 0.35 (0.19), residues: 750 sheet: -0.98 (0.23), residues: 456 loop : -0.50 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 162 HIS 0.005 0.001 HIS B 12 PHE 0.010 0.002 PHE B 253 TYR 0.012 0.002 TYR C 54 ARG 0.004 0.001 ARG E 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 345 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7515 (ttp80) REVERT: A 176 LYS cc_start: 0.6850 (OUTLIER) cc_final: 0.6621 (mptt) REVERT: C 176 LYS cc_start: 0.6796 (OUTLIER) cc_final: 0.6501 (mttp) REVERT: D 176 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.6436 (mttp) REVERT: F 176 LYS cc_start: 0.6810 (OUTLIER) cc_final: 0.6601 (mptt) outliers start: 67 outliers final: 41 residues processed: 382 average time/residue: 1.2330 time to fit residues: 519.8615 Evaluate side-chains 365 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 320 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 186 ASN B 75 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 75 ASN C 133 GLN C 186 ASN C 263 ASN D 75 ASN D 186 ASN D 263 ASN E 75 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS F 75 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN F 283 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15084 Z= 0.373 Angle : 0.762 8.450 20472 Z= 0.360 Chirality : 0.051 0.175 2406 Planarity : 0.005 0.035 2568 Dihedral : 15.080 156.935 2152 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.62 % Allowed : 21.66 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.19), residues: 1884 helix: -0.06 (0.19), residues: 750 sheet: -1.43 (0.23), residues: 456 loop : -0.64 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 162 HIS 0.005 0.001 HIS D 12 PHE 0.012 0.003 PHE A 253 TYR 0.018 0.002 TYR D 54 ARG 0.005 0.001 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 324 time to evaluate : 1.635 Fit side-chains revert: symmetry clash REVERT: A 78 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7088 (tptp) REVERT: A 176 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6688 (mptt) REVERT: B 231 HIS cc_start: 0.7392 (m90) cc_final: 0.7175 (m90) REVERT: C 153 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7651 (tttm) REVERT: C 176 LYS cc_start: 0.6775 (OUTLIER) cc_final: 0.6395 (mttp) REVERT: D 153 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7683 (tttm) REVERT: D 176 LYS cc_start: 0.6682 (OUTLIER) cc_final: 0.6404 (mttp) REVERT: E 3 ASN cc_start: 0.6297 (m-40) cc_final: 0.6085 (m110) REVERT: E 153 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7906 (tmtm) REVERT: E 231 HIS cc_start: 0.7374 (m90) cc_final: 0.7152 (m90) REVERT: F 78 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7100 (tptp) REVERT: F 302 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6780 (mpt180) outliers start: 90 outliers final: 45 residues processed: 373 average time/residue: 1.2228 time to fit residues: 503.5450 Evaluate side-chains 357 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 303 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Chi-restraints excluded: chain F residue 302 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.5980 chunk 161 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 186 ASN A 283 HIS B 75 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 186 ASN C 263 ASN D 186 ASN D 263 ASN E 75 ASN E 283 HIS F 186 ASN F 263 ASN F 283 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15084 Z= 0.205 Angle : 0.669 7.815 20472 Z= 0.306 Chirality : 0.047 0.161 2406 Planarity : 0.003 0.030 2568 Dihedral : 14.488 160.581 2152 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.49 % Allowed : 22.78 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.19), residues: 1884 helix: 0.21 (0.19), residues: 750 sheet: -1.51 (0.23), residues: 456 loop : -0.57 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 154 HIS 0.003 0.001 HIS F 12 PHE 0.007 0.001 PHE D 138 TYR 0.011 0.002 TYR D 54 ARG 0.003 0.000 ARG F 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 315 time to evaluate : 1.563 Fit side-chains revert: symmetry clash REVERT: A 176 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6624 (mptt) REVERT: B 153 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7889 (tmtm) REVERT: B 231 HIS cc_start: 0.7376 (m90) cc_final: 0.7170 (m90) REVERT: B 272 THR cc_start: 0.7835 (p) cc_final: 0.7627 (p) REVERT: C 153 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7626 (tttm) REVERT: C 176 LYS cc_start: 0.6747 (OUTLIER) cc_final: 0.6426 (mptt) REVERT: C 288 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.6998 (mt0) REVERT: D 99 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7889 (ptpt) REVERT: D 153 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7641 (tttm) REVERT: E 231 HIS cc_start: 0.7365 (m90) cc_final: 0.7161 (m90) outliers start: 72 outliers final: 44 residues processed: 357 average time/residue: 1.2354 time to fit residues: 486.7845 Evaluate side-chains 358 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 307 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 263 ASN Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 112 optimal weight: 0.3980 chunk 109 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 186 ASN A 283 HIS B 75 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 133 GLN C 186 ASN C 263 ASN D 186 ASN D 263 ASN E 75 ASN E 283 HIS F 186 ASN F 263 ASN F 283 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15084 Z= 0.198 Angle : 0.660 7.573 20472 Z= 0.300 Chirality : 0.046 0.153 2406 Planarity : 0.003 0.028 2568 Dihedral : 13.874 162.857 2152 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.56 % Allowed : 23.47 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1884 helix: 0.36 (0.19), residues: 750 sheet: -1.44 (0.23), residues: 456 loop : -0.57 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 154 HIS 0.003 0.001 HIS F 283 PHE 0.008 0.001 PHE F 138 TYR 0.011 0.001 TYR C 54 ARG 0.006 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 310 time to evaluate : 1.621 Fit side-chains revert: symmetry clash REVERT: A 176 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6537 (mptt) REVERT: B 231 HIS cc_start: 0.7365 (m90) cc_final: 0.7151 (m90) REVERT: C 153 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7629 (tttm) REVERT: C 176 LYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6496 (mptt) REVERT: C 288 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.6975 (mt0) REVERT: D 99 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7746 (ptpt) REVERT: D 288 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.6968 (mt0) REVERT: E 231 HIS cc_start: 0.7334 (m90) cc_final: 0.7099 (m90) REVERT: F 298 GLU cc_start: 0.6600 (mp0) cc_final: 0.6392 (mp0) outliers start: 73 outliers final: 49 residues processed: 354 average time/residue: 1.2597 time to fit residues: 491.5549 Evaluate side-chains 368 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 313 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 288 GLN Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 0.0980 chunk 122 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 186 ASN A 283 HIS B 75 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 186 ASN C 263 ASN D 186 ASN D 263 ASN E 75 ASN E 283 HIS F 75 ASN F 186 ASN F 263 ASN F 283 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15084 Z= 0.204 Angle : 0.665 10.207 20472 Z= 0.302 Chirality : 0.046 0.153 2406 Planarity : 0.003 0.044 2568 Dihedral : 13.488 163.219 2152 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.00 % Allowed : 24.09 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.19), residues: 1884 helix: 0.41 (0.19), residues: 750 sheet: -1.40 (0.24), residues: 456 loop : -0.59 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 154 HIS 0.003 0.001 HIS B 283 PHE 0.008 0.001 PHE F 138 TYR 0.011 0.002 TYR C 54 ARG 0.007 0.000 ARG C 302 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 318 time to evaluate : 1.745 Fit side-chains revert: symmetry clash REVERT: A 176 LYS cc_start: 0.6780 (OUTLIER) cc_final: 0.6543 (mptt) REVERT: B 231 HIS cc_start: 0.7363 (m90) cc_final: 0.7129 (m90) REVERT: C 153 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7619 (tttm) REVERT: C 176 LYS cc_start: 0.6761 (OUTLIER) cc_final: 0.6500 (mptt) REVERT: C 288 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.6996 (mt0) REVERT: D 99 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7729 (ptpt) REVERT: D 288 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.6994 (mt0) REVERT: E 231 HIS cc_start: 0.7334 (m90) cc_final: 0.7107 (m90) outliers start: 64 outliers final: 44 residues processed: 355 average time/residue: 1.2174 time to fit residues: 477.9727 Evaluate side-chains 370 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 320 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 288 GLN Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 72 optimal weight: 0.0980 chunk 131 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 186 ASN A 283 HIS B 75 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 75 ASN C 186 ASN D 186 ASN E 75 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS F 75 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN F 283 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15084 Z= 0.207 Angle : 0.667 7.717 20472 Z= 0.304 Chirality : 0.046 0.154 2406 Planarity : 0.003 0.027 2568 Dihedral : 12.886 163.416 2152 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.75 % Allowed : 24.41 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1884 helix: 0.38 (0.19), residues: 750 sheet: -1.47 (0.23), residues: 468 loop : -0.55 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 154 HIS 0.003 0.001 HIS F 283 PHE 0.008 0.001 PHE F 138 TYR 0.012 0.002 TYR C 54 ARG 0.007 0.000 ARG C 302 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 324 time to evaluate : 1.803 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7898 (ttp-110) cc_final: 0.7494 (ttp80) REVERT: A 176 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6551 (mptt) REVERT: B 231 HIS cc_start: 0.7365 (m90) cc_final: 0.7134 (m90) REVERT: C 176 LYS cc_start: 0.6739 (OUTLIER) cc_final: 0.6504 (mptt) REVERT: C 288 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.6992 (mt0) REVERT: D 99 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7799 (ptpt) REVERT: D 288 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7013 (mt0) REVERT: E 231 HIS cc_start: 0.7334 (m90) cc_final: 0.7111 (m90) outliers start: 60 outliers final: 43 residues processed: 360 average time/residue: 1.2541 time to fit residues: 498.5228 Evaluate side-chains 367 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 319 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 288 GLN Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 0.2980 chunk 90 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 186 ASN A 283 HIS B 75 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN E 75 ASN E 283 HIS F 75 ASN F 186 ASN F 283 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15084 Z= 0.214 Angle : 0.670 7.413 20472 Z= 0.307 Chirality : 0.046 0.155 2406 Planarity : 0.003 0.053 2568 Dihedral : 12.707 163.307 2152 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.56 % Allowed : 24.72 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 1884 helix: 0.36 (0.19), residues: 750 sheet: -1.48 (0.23), residues: 468 loop : -0.56 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 154 HIS 0.004 0.001 HIS A 283 PHE 0.008 0.001 PHE F 138 TYR 0.017 0.002 TYR F 94 ARG 0.011 0.000 ARG C 302 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 323 time to evaluate : 1.730 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7895 (ttp-110) cc_final: 0.7496 (ttp80) REVERT: A 176 LYS cc_start: 0.6779 (OUTLIER) cc_final: 0.6497 (mptt) REVERT: B 176 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6279 (mttp) REVERT: B 231 HIS cc_start: 0.7368 (m90) cc_final: 0.7140 (m90) REVERT: C 176 LYS cc_start: 0.6746 (OUTLIER) cc_final: 0.6499 (mptt) REVERT: C 288 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.6988 (mt0) REVERT: D 99 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7830 (ptpt) REVERT: D 288 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7013 (mt0) REVERT: E 231 HIS cc_start: 0.7338 (m90) cc_final: 0.7120 (m90) outliers start: 57 outliers final: 42 residues processed: 358 average time/residue: 1.2556 time to fit residues: 501.9806 Evaluate side-chains 370 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 322 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 288 GLN Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 61 optimal weight: 0.0270 chunk 151 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 186 ASN A 283 HIS B 75 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 75 ASN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN E 75 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS F 75 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN F 283 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4991 r_free = 0.4991 target = 0.265824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.250704 restraints weight = 13332.144| |-----------------------------------------------------------------------------| r_work (start): 0.4893 rms_B_bonded: 0.80 r_work: 0.4834 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.4735 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.4735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15084 Z= 0.215 Angle : 0.674 9.039 20472 Z= 0.309 Chirality : 0.046 0.160 2406 Planarity : 0.003 0.042 2568 Dihedral : 12.664 163.245 2152 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.56 % Allowed : 24.72 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.19), residues: 1884 helix: 0.40 (0.19), residues: 744 sheet: -1.46 (0.23), residues: 468 loop : -0.62 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 154 HIS 0.005 0.001 HIS A 283 PHE 0.008 0.001 PHE F 138 TYR 0.018 0.002 TYR F 94 ARG 0.012 0.000 ARG C 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7570.07 seconds wall clock time: 136 minutes 54.13 seconds (8214.13 seconds total)