Starting phenix.real_space_refine on Sat Mar 16 15:39:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbe_27281/03_2024/8dbe_27281_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbe_27281/03_2024/8dbe_27281.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbe_27281/03_2024/8dbe_27281_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbe_27281/03_2024/8dbe_27281_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbe_27281/03_2024/8dbe_27281_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbe_27281/03_2024/8dbe_27281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbe_27281/03_2024/8dbe_27281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbe_27281/03_2024/8dbe_27281_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbe_27281/03_2024/8dbe_27281_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.289 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 9252 2.51 5 N 2628 2.21 5 O 2958 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14982 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "B" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "C" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "D" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "E" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "F" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {' MG': 2, 'ADP': 3, 'HSX': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' MG': 2, 'ADP': 1, 'HSX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {' MG': 2, 'ADP': 2, 'HSX': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {' MG': 2, 'ADP': 2, 'HSX': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {' MG': 2, 'ADP': 3, 'HSX': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' MG': 2, 'ADP': 1, 'HSX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 8.33, per 1000 atoms: 0.56 Number of scatterers: 14982 At special positions: 0 Unit cell: (120.549, 127.293, 76.713, 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 2958 8.00 N 2628 7.00 C 9252 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: 5.98 Conformation dependent library (CDL) restraints added in 2.8 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: 2.62 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: 4.553A pdb=" N ILE A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.707A 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: 4.553A 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: 4.563A 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: 4.554A pdb=" N ILE C 258 " --> pdb=" O GLY C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.707A 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: 4.563A 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: 4.553A pdb=" N ILE E 258 " --> pdb=" O GLY E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.707A 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: 4.553A 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: 6.362A 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: 7.565A pdb=" N ILE A 55 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.577A 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: 7.979A 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: 7.885A 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: 7.443A 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: 7.804A 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: 6.573A pdb=" N LEU A 248 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.500A 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: 6.255A 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: 6.081A pdb=" N VAL A 168 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 8.314A 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: 6.277A 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: 6.362A pdb=" N TYR B 54 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.179A 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: 6.674A pdb=" N HIS B 123 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE B 89 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE B 125 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR B 126 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 5.836A 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: 7.885A 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: 6.501A pdb=" N ALA B 216 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.255A 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: 7.296A pdb=" N VAL B 219 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL B 168 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP B 188 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N SER B 169 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 6.925A 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: 7.541A pdb=" N PHE C 7 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR C 54 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.179A 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: 6.577A pdb=" N THR C 86 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.675A 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: 7.979A pdb=" N THR C 126 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 5.837A 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: 7.885A pdb=" N GLN C 288 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 6.125A 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: 6.630A 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: 6.573A pdb=" N LEU C 248 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 216 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 7.671A 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: 7.295A pdb=" N VAL C 219 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL C 168 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.903A 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: 7.541A pdb=" N PHE D 7 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR D 54 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG D 84 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE D 55 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR D 86 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.675A 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: 7.979A pdb=" N THR D 126 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 5.837A 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: 6.124A pdb=" N VAL D 269 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE D 290 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL D 271 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL D 244 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL D 269 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA D 246 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL D 271 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU D 248 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA D 216 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE D 247 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.255A 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: 7.295A pdb=" N VAL D 219 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL D 168 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.903A 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: 6.277A 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: 6.362A 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: 7.566A pdb=" N ILE E 55 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR E 86 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.674A 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: 6.143A 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: 5.836A 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: 7.885A pdb=" N GLN E 288 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL E 269 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.443A 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: 6.630A 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: 6.573A 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: 7.670A pdb=" N ILE E 247 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.255A 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: 7.296A pdb=" N VAL E 219 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL E 168 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 6.903A 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: 6.925A 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: 7.541A pdb=" N PHE F 7 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 6.362A 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: 7.565A pdb=" N ILE F 55 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.577A 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: 7.369A pdb=" N ILE F 89 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE F 125 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR F 126 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 5.837A 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: 7.443A 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: 7.804A pdb=" N VAL F 244 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 6.629A 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: 5.439A pdb=" N VAL F 271 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 6.573A 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: 6.081A pdb=" N VAL F 168 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 8.314A 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: 4.56 Time building geometry restraints manager: 6.48 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: 4974 1.34 - 1.46: 2178 1.46 - 1.57: 7824 1.57 - 1.69: 42 1.69 - 1.81: 150 Bond restraints: 15168 Sorted by residual: bond pdb=" C1' ADP C 402 " pdb=" C2' ADP C 402 " ideal model delta sigma weight residual 1.306 1.534 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ADP F 402 " pdb=" C2' ADP F 402 " ideal model delta sigma weight residual 1.306 1.534 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ADP A 402 " pdb=" C2' ADP A 402 " ideal model delta sigma weight residual 1.306 1.534 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ADP B 402 " pdb=" C2' ADP B 402 " ideal model delta sigma weight residual 1.306 1.534 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ADP E 402 " pdb=" C2' ADP E 402 " ideal model delta sigma weight residual 1.306 1.534 -0.228 2.00e-02 2.50e+03 1.30e+02 ... (remaining 15163 not shown) Histogram of bond angle deviations from ideal: 98.68 - 106.02: 366 106.02 - 113.36: 8917 113.36 - 120.69: 6266 120.69 - 128.03: 4905 128.03 - 135.37: 138 Bond angle restraints: 20592 Sorted by residual: angle pdb=" PA ADP F 402 " pdb=" O3A ADP F 402 " pdb=" PB ADP F 402 " ideal model delta sigma weight residual 123.64 135.37 -11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" PA ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PB ADP B 402 " ideal model delta sigma weight residual 123.64 135.36 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" PA ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PB ADP C 402 " ideal model delta sigma weight residual 123.64 135.36 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" PA ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PB ADP E 402 " ideal model delta sigma weight residual 123.64 135.35 -11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" PA ADP A 402 " pdb=" O3A ADP A 402 " pdb=" PB ADP A 402 " ideal model delta sigma weight residual 123.64 135.34 -11.70 3.00e+00 1.11e-01 1.52e+01 ... (remaining 20587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8221 17.96 - 35.93: 713 35.93 - 53.89: 207 53.89 - 71.86: 96 71.86 - 89.82: 57 Dihedral angle restraints: 9294 sinusoidal: 3786 harmonic: 5508 Sorted by residual: dihedral pdb=" CA SER E 8 " pdb=" C SER E 8 " pdb=" N GLY E 9 " pdb=" CA GLY E 9 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA SER F 8 " pdb=" C SER F 8 " pdb=" N GLY F 9 " pdb=" CA GLY F 9 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA SER A 8 " pdb=" C SER A 8 " pdb=" N GLY A 9 " pdb=" CA GLY A 9 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 9291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1197 0.032 - 0.065: 711 0.065 - 0.097: 273 0.097 - 0.129: 160 0.129 - 0.162: 17 Chirality restraints: 2358 Sorted by residual: chirality pdb=" CA ILE C 275 " pdb=" N ILE C 275 " pdb=" C ILE C 275 " pdb=" CB ILE C 275 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA ILE B 275 " pdb=" N ILE B 275 " pdb=" C ILE B 275 " pdb=" CB ILE B 275 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA ILE E 275 " pdb=" N ILE E 275 " pdb=" C ILE E 275 " pdb=" CB ILE E 275 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 2355 not shown) Planarity restraints: 2592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 HSX E 401 " -0.249 2.00e-02 2.50e+03 6.60e-01 9.81e+03 pdb=" C2 HSX E 401 " -0.886 2.00e-02 2.50e+03 pdb=" C3 HSX E 401 " -0.025 2.00e-02 2.50e+03 pdb=" C4 HSX E 401 " 0.319 2.00e-02 2.50e+03 pdb=" C5 HSX E 401 " -0.478 2.00e-02 2.50e+03 pdb=" O1 HSX E 401 " 0.877 2.00e-02 2.50e+03 pdb=" O2 HSX E 401 " -0.806 2.00e-02 2.50e+03 pdb=" O3 HSX E 401 " 1.148 2.00e-02 2.50e+03 pdb=" O4 HSX E 401 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX F 401 " 0.249 2.00e-02 2.50e+03 6.60e-01 9.81e+03 pdb=" C2 HSX F 401 " 0.886 2.00e-02 2.50e+03 pdb=" C3 HSX F 401 " 0.025 2.00e-02 2.50e+03 pdb=" C4 HSX F 401 " -0.319 2.00e-02 2.50e+03 pdb=" C5 HSX F 401 " 0.478 2.00e-02 2.50e+03 pdb=" O1 HSX F 401 " -0.877 2.00e-02 2.50e+03 pdb=" O2 HSX F 401 " 0.806 2.00e-02 2.50e+03 pdb=" O3 HSX F 401 " -1.148 2.00e-02 2.50e+03 pdb=" O4 HSX F 401 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX A 401 " 0.249 2.00e-02 2.50e+03 6.60e-01 9.81e+03 pdb=" C2 HSX A 401 " 0.886 2.00e-02 2.50e+03 pdb=" C3 HSX A 401 " 0.025 2.00e-02 2.50e+03 pdb=" C4 HSX A 401 " -0.319 2.00e-02 2.50e+03 pdb=" C5 HSX A 401 " 0.478 2.00e-02 2.50e+03 pdb=" O1 HSX A 401 " -0.877 2.00e-02 2.50e+03 pdb=" O2 HSX A 401 " 0.806 2.00e-02 2.50e+03 pdb=" O3 HSX A 401 " -1.148 2.00e-02 2.50e+03 pdb=" O4 HSX A 401 " -0.100 2.00e-02 2.50e+03 ... (remaining 2589 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 126 2.47 - 3.08: 11020 3.08 - 3.69: 24501 3.69 - 4.29: 38008 4.29 - 4.90: 60004 Nonbonded interactions: 133659 Sorted by model distance: nonbonded pdb="MG MG B 403 " pdb=" O HOH B 505 " model vdw 1.867 2.170 nonbonded pdb="MG MG E 404 " pdb=" O HOH E 509 " model vdw 1.867 2.170 nonbonded pdb="MG MG F 403 " pdb=" O HOH F 505 " model vdw 1.867 2.170 nonbonded pdb="MG MG A 404 " pdb=" O HOH A 509 " model vdw 1.867 2.170 nonbonded pdb="MG MG C 404 " pdb=" O HOH C 507 " model vdw 1.867 2.170 ... (remaining 133654 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 401 through 402 or resid 404)) selection = (chain 'B' and (resid 2 through 317 or resid 401 through 402 or resid 404)) selection = (chain 'C' and (resid 2 through 317 or resid 401 through 402 or resid 404)) selection = (chain 'D' and (resid 2 through 317 or resid 401 through 402 or resid 404)) selection = (chain 'E' and (resid 2 through 317 or resid 401 through 402 or resid 404)) selection = (chain 'F' and (resid 2 through 317 or resid 401 through 402 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.450 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 42.330 Find NCS groups from input model: 1.150 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:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 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 : 0.014 0.228 15168 Z= 0.931 Angle : 0.988 11.731 20592 Z= 0.428 Chirality : 0.050 0.162 2358 Planarity : 0.050 0.660 2592 Dihedral : 17.662 89.820 5706 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.05 % Allowed : 14.49 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.19), residues: 1884 helix: 1.88 (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 C 162 HIS 0.007 0.001 HIS C 12 PHE 0.012 0.002 PHE C 138 TYR 0.011 0.002 TYR B 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 397 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 348 time to evaluate : 1.680 Fit side-chains REVERT: B 281 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8244 (mtm) REVERT: C 242 THR cc_start: 0.8919 (p) cc_final: 0.8700 (p) REVERT: C 281 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8265 (mtm) REVERT: C 283 HIS cc_start: 0.8523 (m-70) cc_final: 0.8290 (m-70) REVERT: D 242 THR cc_start: 0.8921 (p) cc_final: 0.8701 (p) REVERT: D 283 HIS cc_start: 0.8523 (m-70) cc_final: 0.8289 (m-70) REVERT: E 281 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8240 (mtm) REVERT: F 38 GLN cc_start: 0.8342 (mm110) cc_final: 0.8113 (mm110) outliers start: 49 outliers final: 12 residues processed: 361 average time/residue: 1.4420 time to fit residues: 564.6143 Evaluate side-chains 287 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 272 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 281 MET Chi-restraints excluded: chain F residue 238 SER 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: 4.9990 chunk 140 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 95 optimal weight: 0.3980 chunk 75 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 288 GLN B 288 GLN C 288 GLN D 288 GLN E 288 GLN F 186 ASN F 288 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15168 Z= 0.196 Angle : 1.774 46.888 20592 Z= 0.624 Chirality : 0.046 0.156 2358 Planarity : 0.004 0.023 2592 Dihedral : 14.755 111.314 2266 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.36 % Allowed : 13.37 % Favored : 84.27 % 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: 0.57 (0.19), residues: 1884 helix: 1.59 (0.21), residues: 708 sheet: -0.62 (0.23), residues: 498 loop : 0.04 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 162 HIS 0.004 0.001 HIS F 12 PHE 0.011 0.001 PHE B 138 TYR 0.005 0.001 TYR F 311 ARG 0.005 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 335 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 297 time to evaluate : 1.722 Fit side-chains REVERT: A 13 GLN cc_start: 0.8164 (tp40) cc_final: 0.7928 (tp-100) REVERT: C 242 THR cc_start: 0.8971 (p) cc_final: 0.8742 (p) REVERT: C 283 HIS cc_start: 0.8464 (m-70) cc_final: 0.8256 (m-70) REVERT: D 242 THR cc_start: 0.8972 (p) cc_final: 0.8745 (p) REVERT: D 283 HIS cc_start: 0.8459 (m-70) cc_final: 0.8249 (m-70) REVERT: E 13 GLN cc_start: 0.8065 (tp40) cc_final: 0.7847 (tp40) REVERT: E 281 MET cc_start: 0.8476 (mtp) cc_final: 0.8227 (mtm) REVERT: F 13 GLN cc_start: 0.8161 (tp40) cc_final: 0.7940 (tp-100) outliers start: 38 outliers final: 25 residues processed: 329 average time/residue: 1.3812 time to fit residues: 495.3082 Evaluate side-chains 295 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 270 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 204 ARG Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR 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: 7.9990 chunk 140 optimal weight: 0.0870 chunk 115 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 169 optimal weight: 0.4980 chunk 182 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN E 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15168 Z= 0.180 Angle : 1.752 46.793 20592 Z= 0.613 Chirality : 0.045 0.162 2358 Planarity : 0.003 0.022 2592 Dihedral : 13.824 102.639 2252 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.55 % Allowed : 13.18 % Favored : 84.27 % 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: 0.58 (0.20), residues: 1884 helix: 1.52 (0.21), residues: 714 sheet: -0.51 (0.24), residues: 492 loop : 0.05 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 162 HIS 0.004 0.001 HIS C 12 PHE 0.011 0.001 PHE E 138 TYR 0.005 0.001 TYR E 146 ARG 0.005 0.000 ARG A 214 *********************** 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 342 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 301 time to evaluate : 1.678 Fit side-chains REVERT: C 242 THR cc_start: 0.8953 (p) cc_final: 0.8709 (p) REVERT: D 242 THR cc_start: 0.8955 (p) cc_final: 0.8714 (p) REVERT: F 21 ASP cc_start: 0.7901 (m-30) cc_final: 0.7557 (m-30) outliers start: 41 outliers final: 27 residues processed: 332 average time/residue: 1.4287 time to fit residues: 515.8122 Evaluate side-chains 321 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 294 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 THR 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 249 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15168 Z= 0.338 Angle : 1.817 46.166 20592 Z= 0.649 Chirality : 0.048 0.153 2358 Planarity : 0.004 0.031 2592 Dihedral : 14.727 114.073 2252 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.74 % Allowed : 13.37 % Favored : 83.89 % 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: 0.12 (0.19), residues: 1884 helix: 1.02 (0.20), residues: 756 sheet: -0.62 (0.23), residues: 492 loop : -0.25 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 162 HIS 0.006 0.001 HIS D 12 PHE 0.014 0.002 PHE E 138 TYR 0.009 0.002 TYR F 311 ARG 0.005 0.001 ARG F 214 *********************** 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 347 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 303 time to evaluate : 1.665 Fit side-chains REVERT: D 242 THR cc_start: 0.9003 (p) cc_final: 0.8747 (p) REVERT: F 68 MET cc_start: 0.8460 (tpp) cc_final: 0.8238 (tpp) outliers start: 44 outliers final: 34 residues processed: 335 average time/residue: 1.3792 time to fit residues: 503.3876 Evaluate side-chains 330 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 296 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 161 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15168 Z= 0.197 Angle : 1.761 46.775 20592 Z= 0.619 Chirality : 0.046 0.159 2358 Planarity : 0.004 0.027 2592 Dihedral : 14.110 112.917 2250 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.30 % Allowed : 13.74 % Favored : 83.96 % 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: 0.15 (0.19), residues: 1884 helix: 1.05 (0.20), residues: 756 sheet: -0.59 (0.23), residues: 492 loop : -0.26 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 162 HIS 0.005 0.001 HIS D 12 PHE 0.013 0.001 PHE B 138 TYR 0.007 0.001 TYR E 146 ARG 0.005 0.000 ARG F 214 *********************** 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 346 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 309 time to evaluate : 1.766 Fit side-chains REVERT: A 21 ASP cc_start: 0.7908 (m-30) cc_final: 0.7589 (m-30) REVERT: A 68 MET cc_start: 0.8427 (tpp) cc_final: 0.8225 (tpp) REVERT: B 21 ASP cc_start: 0.7995 (m-30) cc_final: 0.7613 (m-30) REVERT: B 281 MET cc_start: 0.8539 (mtp) cc_final: 0.8319 (mtm) REVERT: D 242 THR cc_start: 0.8975 (p) cc_final: 0.8718 (p) outliers start: 37 outliers final: 32 residues processed: 336 average time/residue: 1.4058 time to fit residues: 513.9250 Evaluate side-chains 323 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 291 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15168 Z= 0.345 Angle : 1.820 45.970 20592 Z= 0.651 Chirality : 0.048 0.154 2358 Planarity : 0.004 0.031 2592 Dihedral : 14.812 124.480 2250 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.17 % Allowed : 12.94 % Favored : 83.89 % 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: 0.31 (0.19), residues: 1884 helix: 0.97 (0.20), residues: 756 sheet: -0.60 (0.24), residues: 456 loop : 0.16 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 162 HIS 0.006 0.001 HIS C 12 PHE 0.014 0.002 PHE E 138 TYR 0.011 0.002 TYR F 311 ARG 0.006 0.001 ARG A 22 *********************** 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 344 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 293 time to evaluate : 1.747 Fit side-chains REVERT: A 68 MET cc_start: 0.8457 (tpp) cc_final: 0.8244 (tpp) REVERT: B 62 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7370 (mm-30) REVERT: D 68 MET cc_start: 0.8466 (tpp) cc_final: 0.8257 (tpp) REVERT: F 68 MET cc_start: 0.8525 (tpp) cc_final: 0.8317 (tpp) outliers start: 51 outliers final: 38 residues processed: 329 average time/residue: 1.4129 time to fit residues: 507.7369 Evaluate side-chains 327 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 289 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 314 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.8980 chunk 20 optimal weight: 0.0770 chunk 102 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15168 Z= 0.181 Angle : 1.756 46.821 20592 Z= 0.616 Chirality : 0.045 0.159 2358 Planarity : 0.004 0.029 2592 Dihedral : 14.082 123.797 2250 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.30 % Allowed : 14.05 % Favored : 83.64 % 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: 0.17 (0.19), residues: 1884 helix: 1.04 (0.20), residues: 756 sheet: -0.60 (0.23), residues: 492 loop : -0.22 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 162 HIS 0.007 0.001 HIS F 12 PHE 0.013 0.001 PHE E 138 TYR 0.007 0.001 TYR E 146 ARG 0.006 0.000 ARG A 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 335 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 298 time to evaluate : 1.877 Fit side-chains REVERT: A 21 ASP cc_start: 0.7909 (m-30) cc_final: 0.7625 (m-30) REVERT: B 21 ASP cc_start: 0.8010 (m-30) cc_final: 0.7645 (m-30) REVERT: B 281 MET cc_start: 0.8584 (mtp) cc_final: 0.8356 (mtm) REVERT: C 21 ASP cc_start: 0.8044 (m-30) cc_final: 0.7662 (m-30) REVERT: D 21 ASP cc_start: 0.8056 (m-30) cc_final: 0.7668 (m-30) REVERT: E 21 ASP cc_start: 0.8019 (m-30) cc_final: 0.7655 (m-30) REVERT: E 38 GLN cc_start: 0.8443 (mm110) cc_final: 0.8167 (mm110) REVERT: F 21 ASP cc_start: 0.7905 (m-30) cc_final: 0.7635 (m-30) REVERT: F 68 MET cc_start: 0.8475 (tpp) cc_final: 0.8264 (tpp) outliers start: 37 outliers final: 31 residues processed: 323 average time/residue: 1.4065 time to fit residues: 494.5248 Evaluate side-chains 322 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 291 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.0670 chunk 113 optimal weight: 0.0020 chunk 122 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 0.0980 chunk 140 optimal weight: 0.5980 overall best weight: 0.3126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15168 Z= 0.156 Angle : 1.745 47.114 20592 Z= 0.608 Chirality : 0.045 0.158 2358 Planarity : 0.003 0.027 2592 Dihedral : 13.330 113.293 2250 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.99 % Allowed : 14.43 % Favored : 83.58 % 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: 0.31 (0.19), residues: 1884 helix: 1.16 (0.20), residues: 756 sheet: -0.48 (0.24), residues: 492 loop : -0.17 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 162 HIS 0.005 0.001 HIS B 12 PHE 0.012 0.001 PHE B 138 TYR 0.007 0.001 TYR E 146 ARG 0.007 0.000 ARG F 214 *********************** 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 337 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 305 time to evaluate : 1.551 Fit side-chains REVERT: A 21 ASP cc_start: 0.7853 (m-30) cc_final: 0.7569 (m-30) REVERT: B 21 ASP cc_start: 0.7968 (m-30) cc_final: 0.7620 (m-30) REVERT: B 281 MET cc_start: 0.8519 (mtp) cc_final: 0.8279 (mtm) REVERT: C 17 GLN cc_start: 0.8961 (tp40) cc_final: 0.8633 (tp-100) REVERT: C 21 ASP cc_start: 0.8015 (m-30) cc_final: 0.7668 (m-30) REVERT: D 17 GLN cc_start: 0.8966 (tp40) cc_final: 0.8691 (tp-100) REVERT: D 21 ASP cc_start: 0.8045 (m-30) cc_final: 0.7776 (m-30) REVERT: E 21 ASP cc_start: 0.7988 (m-30) cc_final: 0.7652 (m-30) REVERT: F 21 ASP cc_start: 0.7871 (m-30) cc_final: 0.7600 (m-30) outliers start: 32 outliers final: 23 residues processed: 326 average time/residue: 1.3484 time to fit residues: 480.2608 Evaluate side-chains 316 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 293 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 3.9990 chunk 171 optimal weight: 0.0770 chunk 156 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 51 optimal weight: 0.0470 chunk 150 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15168 Z= 0.176 Angle : 1.756 46.932 20592 Z= 0.615 Chirality : 0.045 0.159 2358 Planarity : 0.003 0.031 2592 Dihedral : 13.097 108.133 2250 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.68 % Allowed : 15.36 % Favored : 82.96 % 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: 0.34 (0.19), residues: 1884 helix: 1.17 (0.20), residues: 756 sheet: -0.48 (0.24), residues: 492 loop : -0.13 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 162 HIS 0.007 0.001 HIS C 12 PHE 0.012 0.001 PHE E 138 TYR 0.009 0.001 TYR E 146 ARG 0.008 0.000 ARG D 22 *********************** 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 323 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 296 time to evaluate : 1.912 Fit side-chains REVERT: A 21 ASP cc_start: 0.7879 (m-30) cc_final: 0.7570 (m-30) REVERT: B 21 ASP cc_start: 0.7992 (m-30) cc_final: 0.7656 (m-30) REVERT: B 281 MET cc_start: 0.8583 (mtp) cc_final: 0.8322 (mtm) REVERT: C 21 ASP cc_start: 0.8017 (m-30) cc_final: 0.7653 (m-30) REVERT: D 21 ASP cc_start: 0.8027 (m-30) cc_final: 0.7663 (m-30) REVERT: E 21 ASP cc_start: 0.8001 (m-30) cc_final: 0.7660 (m-30) REVERT: F 21 ASP cc_start: 0.7885 (m-30) cc_final: 0.7600 (m-30) outliers start: 27 outliers final: 23 residues processed: 314 average time/residue: 1.4167 time to fit residues: 490.3337 Evaluate side-chains 322 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 299 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 185 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15168 Z= 0.243 Angle : 1.784 46.724 20592 Z= 0.631 Chirality : 0.047 0.157 2358 Planarity : 0.004 0.033 2592 Dihedral : 13.482 113.426 2249 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.80 % Allowed : 15.49 % Favored : 82.71 % 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: 0.46 (0.19), residues: 1884 helix: 1.09 (0.20), residues: 756 sheet: -0.46 (0.24), residues: 456 loop : 0.20 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 162 HIS 0.008 0.001 HIS C 12 PHE 0.012 0.002 PHE E 138 TYR 0.011 0.001 TYR E 146 ARG 0.007 0.000 ARG D 22 ********************** 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 326 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 297 time to evaluate : 1.699 Fit side-chains REVERT: B 21 ASP cc_start: 0.7988 (m-30) cc_final: 0.7625 (m-30) REVERT: C 21 ASP cc_start: 0.8048 (m-30) cc_final: 0.7679 (m-30) REVERT: D 21 ASP cc_start: 0.8033 (m-30) cc_final: 0.7682 (m-30) REVERT: E 21 ASP cc_start: 0.7999 (m-30) cc_final: 0.7630 (m-30) REVERT: F 21 ASP cc_start: 0.7910 (m-30) cc_final: 0.7615 (m-30) outliers start: 29 outliers final: 28 residues processed: 318 average time/residue: 1.3860 time to fit residues: 480.1997 Evaluate side-chains 321 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 293 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 314 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 147 optimal weight: 0.3980 chunk 61 optimal weight: 0.0980 chunk 151 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.0170 overall best weight: 0.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.106091 restraints weight = 13853.783| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.17 r_work: 0.3099 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15168 Z= 0.177 Angle : 1.757 47.036 20592 Z= 0.616 Chirality : 0.045 0.160 2358 Planarity : 0.003 0.030 2592 Dihedral : 12.881 103.879 2249 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.80 % Allowed : 15.36 % Favored : 82.84 % 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: 0.28 (0.19), residues: 1884 helix: 1.12 (0.20), residues: 756 sheet: -0.49 (0.24), residues: 492 loop : -0.17 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 162 HIS 0.007 0.001 HIS C 12 PHE 0.012 0.001 PHE E 138 TYR 0.010 0.001 TYR E 146 ARG 0.007 0.000 ARG D 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7489.54 seconds wall clock time: 132 minutes 1.20 seconds (7921.20 seconds total)