Starting phenix.real_space_refine on Fri Mar 15 15:08:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfm_0877/03_2024/6lfm_0877_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfm_0877/03_2024/6lfm_0877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfm_0877/03_2024/6lfm_0877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfm_0877/03_2024/6lfm_0877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfm_0877/03_2024/6lfm_0877_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfm_0877/03_2024/6lfm_0877_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1821 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6510 2.51 5 N 1744 2.21 5 O 1855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10181 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1805 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2579 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 582 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "E" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 551 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "R" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2451 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 295} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1750 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.83, per 1000 atoms: 0.57 Number of scatterers: 10181 At special positions: 0 Unit cell: (87.3602, 123.414, 156.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1855 8.00 N 1744 7.00 C 6510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 34 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 50 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 34 " distance=2.04 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 50 " distance=2.04 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.04 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 3.96 Conformation dependent library (CDL) restraints added in 1.9 seconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2448 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 16 sheets defined 31.3% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.561A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 17 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.866A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 51' Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.527A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 removed outlier: 3.917A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 removed outlier: 4.228A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 307 removed outlier: 3.524A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.841A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 23 removed outlier: 4.062A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.946A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.510A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 21 No H-bonds generated for 'chain 'D' and resid 19 through 21' Processing helix chain 'D' and resid 57 through 71 removed outlier: 4.861A pdb=" N VAL D 62 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU D 63 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE D 65 " --> pdb=" O VAL D 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 59 No H-bonds generated for 'chain 'E' and resid 56 through 59' Processing helix chain 'E' and resid 61 through 69 Processing helix chain 'R' and resid 47 through 59 removed outlier: 4.255A pdb=" N VAL R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 74 removed outlier: 4.424A pdb=" N ASN R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU R 68 " --> pdb=" O LEU R 64 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET R 70 " --> pdb=" O ASN R 66 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU R 74 " --> pdb=" O MET R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 97 removed outlier: 4.136A pdb=" N LEU R 87 " --> pdb=" O THR R 83 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU R 88 " --> pdb=" O ASP R 84 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 108 removed outlier: 3.649A pdb=" N SER R 107 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS R 108 " --> pdb=" O TRP R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 135 removed outlier: 3.706A pdb=" N SER R 123 " --> pdb=" O CYS R 119 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU R 124 " --> pdb=" O LYS R 120 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN R 129 " --> pdb=" O LEU R 125 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR R 131 " --> pdb=" O GLU R 127 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE R 134 " --> pdb=" O PHE R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 146 Processing helix chain 'R' and resid 154 through 160 removed outlier: 3.869A pdb=" N LYS R 158 " --> pdb=" O LEU R 155 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 176 Processing helix chain 'R' and resid 178 through 181 No H-bonds generated for 'chain 'R' and resid 178 through 181' Processing helix chain 'R' and resid 208 through 213 removed outlier: 3.644A pdb=" N ILE R 213 " --> pdb=" O MET R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 218 No H-bonds generated for 'chain 'R' and resid 215 through 218' Processing helix chain 'R' and resid 221 through 228 Processing helix chain 'R' and resid 231 through 240 Processing helix chain 'R' and resid 246 through 279 removed outlier: 4.093A pdb=" N ARG R 251 " --> pdb=" O HIS R 247 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA R 255 " --> pdb=" O ARG R 251 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL R 257 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU R 262 " --> pdb=" O LEU R 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU R 265 " --> pdb=" O LEU R 261 " (cutoff:3.500A) Proline residue: R 266 - end of helix removed outlier: 3.725A pdb=" N LEU R 272 " --> pdb=" O ASN R 268 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR R 275 " --> pdb=" O LEU R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 314 removed outlier: 3.502A pdb=" N ILE R 301 " --> pdb=" O ASP R 297 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N HIS R 306 " --> pdb=" O LEU R 302 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER R 307 " --> pdb=" O GLY R 303 " (cutoff:3.500A) Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 319 through 331 removed outlier: 3.623A pdb=" N LEU R 326 " --> pdb=" O ARG R 322 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE R 328 " --> pdb=" O GLY R 324 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 209 through 211 No H-bonds generated for 'chain 'S' and resid 209 through 211' Processing sheet with id= A, first strand: chain 'A' and resid 34 through 38 removed outlier: 3.834A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 223 through 226 Processing sheet with id= C, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.609A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.753A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.556A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.358A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 295 through 298 removed outlier: 3.627A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.884A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 149 through 153 removed outlier: 3.594A pdb=" N ARG B 150 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 166 through 169 removed outlier: 3.645A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 26 through 28 Processing sheet with id= L, first strand: chain 'E' and resid 22 through 28 removed outlier: 3.610A pdb=" N LYS E 23 " --> pdb=" O LYS E 42 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS E 42 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU E 25 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE E 40 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL E 27 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU E 38 " --> pdb=" O VAL E 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S' and resid 17 through 21 removed outlier: 3.673A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 115 through 117 removed outlier: 6.090A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'S' and resid 144 through 148 Processing sheet with id= P, first strand: chain 'S' and resid 213 through 215 removed outlier: 3.531A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3266 1.34 - 1.46: 2534 1.46 - 1.59: 4490 1.59 - 1.71: 0 1.71 - 1.84: 100 Bond restraints: 10390 Sorted by residual: bond pdb=" C10 CLR R 401 " pdb=" C5 CLR R 401 " ideal model delta sigma weight residual 1.519 1.402 0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C4 CLR R 401 " pdb=" C5 CLR R 401 " ideal model delta sigma weight residual 1.506 1.391 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C6 CLR R 401 " pdb=" C7 CLR R 401 " ideal model delta sigma weight residual 1.492 1.388 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 1.332 1.395 -0.063 2.00e-02 2.50e+03 9.83e+00 bond pdb=" CB VAL B 187 " pdb=" CG2 VAL B 187 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.64e+00 ... (remaining 10385 not shown) Histogram of bond angle deviations from ideal: 96.97 - 104.42: 134 104.42 - 111.86: 4870 111.86 - 119.31: 3807 119.31 - 126.75: 5135 126.75 - 134.20: 133 Bond angle restraints: 14079 Sorted by residual: angle pdb=" N PRO R 30 " pdb=" CA PRO R 30 " pdb=" C PRO R 30 " ideal model delta sigma weight residual 110.70 116.54 -5.84 1.22e+00 6.72e-01 2.29e+01 angle pdb=" CA MET A 240 " pdb=" CB MET A 240 " pdb=" CG MET A 240 " ideal model delta sigma weight residual 114.10 123.46 -9.36 2.00e+00 2.50e-01 2.19e+01 angle pdb=" CA PRO R 30 " pdb=" C PRO R 30 " pdb=" N PRO R 31 " ideal model delta sigma weight residual 117.93 123.42 -5.49 1.20e+00 6.94e-01 2.09e+01 angle pdb=" C CYS A 3 " pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 121.54 129.90 -8.36 1.91e+00 2.74e-01 1.92e+01 angle pdb=" C SER R 190 " pdb=" N ASN R 191 " pdb=" CA ASN R 191 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 ... (remaining 14074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5506 17.56 - 35.11: 621 35.11 - 52.67: 110 52.67 - 70.22: 20 70.22 - 87.78: 16 Dihedral angle restraints: 6273 sinusoidal: 2489 harmonic: 3784 Sorted by residual: dihedral pdb=" CA TYR S 178 " pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta harmonic sigma weight residual 180.00 -132.53 -47.47 0 5.00e+00 4.00e-02 9.01e+01 dihedral pdb=" CB CYS E 9 " pdb=" SG CYS E 9 " pdb=" SG CYS E 50 " pdb=" CB CYS E 50 " ideal model delta sinusoidal sigma weight residual -86.00 -168.56 82.56 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CA GLU R 45 " pdb=" C GLU R 45 " pdb=" N ILE R 46 " pdb=" CA ILE R 46 " ideal model delta harmonic sigma weight residual -180.00 -136.73 -43.27 0 5.00e+00 4.00e-02 7.49e+01 ... (remaining 6270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1434 0.100 - 0.200: 173 0.200 - 0.300: 11 0.300 - 0.400: 2 0.400 - 0.500: 1 Chirality restraints: 1621 Sorted by residual: chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.82 0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" C10 CLR R 401 " pdb=" C1 CLR R 401 " pdb=" C5 CLR R 401 " pdb=" C9 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.85 -2.45 -0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" C17 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C16 CLR R 401 " pdb=" C20 CLR R 401 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 1618 not shown) Planarity restraints: 1768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 30 " -0.067 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO R 31 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO R 31 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 31 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.052 5.00e-02 4.00e+02 7.79e-02 9.72e+00 pdb=" N PRO B 236 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 37 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO R 38 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO R 38 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 38 " 0.037 5.00e-02 4.00e+02 ... (remaining 1765 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2922 2.79 - 3.32: 9014 3.32 - 3.85: 16647 3.85 - 4.37: 19081 4.37 - 4.90: 32809 Nonbonded interactions: 80473 Sorted by model distance: nonbonded pdb=" OG SER B 227 " pdb=" OD1 ASP B 228 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.273 2.440 nonbonded pdb=" OD1 ASP R 94 " pdb=" OG SER R 307 " model vdw 2.280 2.440 nonbonded pdb=" O SER S 192 " pdb=" OG1 THR S 203 " model vdw 2.289 2.440 nonbonded pdb=" ND1 HIS B 54 " pdb=" OG SER B 74 " model vdw 2.308 2.520 ... (remaining 80468 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 'D' and resid 6 through 72) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 2.210 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.350 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.012 0.117 10390 Z= 0.769 Angle : 1.139 13.598 14079 Z= 0.604 Chirality : 0.067 0.500 1621 Planarity : 0.007 0.098 1768 Dihedral : 15.319 87.776 3801 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.27 % Allowed : 9.39 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.60 (0.17), residues: 1284 helix: -4.47 (0.11), residues: 416 sheet: -3.43 (0.26), residues: 278 loop : -3.13 (0.21), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP R 112 HIS 0.009 0.002 HIS A 213 PHE 0.027 0.003 PHE R 97 TYR 0.028 0.003 TYR S 178 ARG 0.006 0.001 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 345 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8374 (ttmt) REVERT: A 243 MET cc_start: 0.8946 (tpp) cc_final: 0.8484 (tpp) REVERT: A 318 GLU cc_start: 0.6789 (tp30) cc_final: 0.5926 (tp30) REVERT: A 341 ASP cc_start: 0.8144 (t0) cc_final: 0.7720 (t0) REVERT: A 346 ASN cc_start: 0.9324 (m-40) cc_final: 0.8991 (m110) REVERT: A 349 LYS cc_start: 0.9043 (tttm) cc_final: 0.8778 (ttpp) REVERT: B 13 GLN cc_start: 0.8750 (mm110) cc_final: 0.7874 (tm-30) REVERT: B 59 TYR cc_start: 0.9000 (m-80) cc_final: 0.8561 (m-80) REVERT: B 101 MET cc_start: 0.9055 (mtp) cc_final: 0.8838 (mtp) REVERT: B 111 TYR cc_start: 0.8978 (m-80) cc_final: 0.8747 (m-10) REVERT: B 172 GLU cc_start: 0.8215 (mp0) cc_final: 0.7943 (mm-30) REVERT: B 188 MET cc_start: 0.7983 (mmm) cc_final: 0.7496 (mmm) REVERT: B 259 GLN cc_start: 0.8380 (pt0) cc_final: 0.7676 (pt0) REVERT: C 13 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.8073 (ptm160) REVERT: C 18 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8403 (tm-30) REVERT: C 20 LYS cc_start: 0.8792 (mttp) cc_final: 0.8274 (ttmm) REVERT: C 27 ARG cc_start: 0.8270 (mtt90) cc_final: 0.7961 (mpt-90) REVERT: D 4 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7772 (mm-30) REVERT: D 13 TYR cc_start: 0.8083 (t80) cc_final: 0.7794 (t80) REVERT: D 20 LYS cc_start: 0.7231 (pptt) cc_final: 0.6983 (pptt) REVERT: D 25 LEU cc_start: 0.8591 (tp) cc_final: 0.8189 (tp) REVERT: D 29 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7245 (tm-30) REVERT: D 32 PRO cc_start: 0.8772 (Cg_endo) cc_final: 0.8543 (Cg_exo) REVERT: E 47 ARG cc_start: 0.6999 (mtt-85) cc_final: 0.6477 (ttm110) REVERT: E 63 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7732 (mp0) REVERT: E 67 LYS cc_start: 0.7782 (mttm) cc_final: 0.7569 (mptt) REVERT: R 50 PHE cc_start: 0.8251 (m-10) cc_final: 0.7968 (m-10) REVERT: R 55 TYR cc_start: 0.8515 (m-80) cc_final: 0.7479 (m-80) REVERT: R 127 GLU cc_start: 0.8892 (tp30) cc_final: 0.8456 (tp30) REVERT: R 174 LEU cc_start: 0.8792 (mm) cc_final: 0.8420 (mm) REVERT: R 228 LEU cc_start: 0.9161 (mm) cc_final: 0.8680 (mm) REVERT: R 287 GLU cc_start: 0.8674 (mm-30) cc_final: 0.7910 (pp20) REVERT: R 310 ASN cc_start: 0.8669 (t0) cc_final: 0.8430 (t0) REVERT: S 73 ASP cc_start: 0.7453 (t0) cc_final: 0.7234 (t0) REVERT: S 83 MET cc_start: 0.8794 (mtm) cc_final: 0.8304 (ptp) REVERT: S 95 TYR cc_start: 0.8723 (m-10) cc_final: 0.8505 (m-10) REVERT: S 125 ASP cc_start: 0.8998 (p0) cc_final: 0.8492 (p0) REVERT: S 130 GLN cc_start: 0.7710 (mt0) cc_final: 0.7296 (mt0) REVERT: S 210 GLU cc_start: 0.7862 (tp30) cc_final: 0.7507 (mm-30) outliers start: 3 outliers final: 0 residues processed: 348 average time/residue: 0.2639 time to fit residues: 121.9140 Evaluate side-chains 270 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 306 GLN B 17 GLN B 62 HIS B 75 GLN B 175 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS R 268 ASN R 323 HIS S 159 ASN S 167 GLN S 171 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10390 Z= 0.280 Angle : 0.680 8.552 14079 Z= 0.357 Chirality : 0.044 0.231 1621 Planarity : 0.005 0.077 1768 Dihedral : 6.361 39.521 1474 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.74 % Allowed : 17.50 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.19), residues: 1284 helix: -2.94 (0.18), residues: 419 sheet: -3.09 (0.26), residues: 291 loop : -2.71 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 112 HIS 0.003 0.001 HIS R 247 PHE 0.019 0.001 PHE R 218 TYR 0.027 0.002 TYR A 302 ARG 0.006 0.000 ARG R 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 307 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8824 (t70) cc_final: 0.8518 (t0) REVERT: A 29 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8356 (ttmt) REVERT: A 243 MET cc_start: 0.8872 (tpp) cc_final: 0.8359 (tpp) REVERT: A 318 GLU cc_start: 0.6760 (tp30) cc_final: 0.5892 (tp30) REVERT: A 341 ASP cc_start: 0.8510 (t0) cc_final: 0.8157 (t0) REVERT: A 346 ASN cc_start: 0.9261 (m-40) cc_final: 0.8933 (m110) REVERT: A 349 LYS cc_start: 0.8980 (tttm) cc_final: 0.8700 (ttpp) REVERT: B 19 ARG cc_start: 0.8340 (ttp-170) cc_final: 0.8058 (ttp-170) REVERT: B 105 TYR cc_start: 0.9088 (t80) cc_final: 0.8585 (t80) REVERT: B 111 TYR cc_start: 0.8930 (m-80) cc_final: 0.8658 (m-10) REVERT: B 157 ILE cc_start: 0.9068 (tt) cc_final: 0.8783 (tt) REVERT: B 172 GLU cc_start: 0.8044 (mp0) cc_final: 0.7819 (mm-30) REVERT: B 188 MET cc_start: 0.7986 (mmm) cc_final: 0.7513 (mmm) REVERT: B 211 TRP cc_start: 0.9264 (m100) cc_final: 0.8717 (m100) REVERT: B 259 GLN cc_start: 0.8157 (pt0) cc_final: 0.7639 (pt0) REVERT: B 297 TRP cc_start: 0.8894 (m100) cc_final: 0.8658 (m100) REVERT: B 303 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8084 (p0) REVERT: C 13 ARG cc_start: 0.8384 (ttm-80) cc_final: 0.8149 (ptp-110) REVERT: C 20 LYS cc_start: 0.8854 (mttp) cc_final: 0.8565 (ttmm) REVERT: C 25 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8523 (mp) REVERT: C 32 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8636 (ttpp) REVERT: D 4 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7754 (mm-30) REVERT: D 13 TYR cc_start: 0.7921 (t80) cc_final: 0.7703 (t80) REVERT: D 28 ILE cc_start: 0.8663 (mt) cc_final: 0.8348 (mm) REVERT: D 29 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7044 (tm-30) REVERT: D 32 PRO cc_start: 0.8564 (Cg_endo) cc_final: 0.8300 (Cg_exo) REVERT: D 68 ARG cc_start: 0.8591 (mmm160) cc_final: 0.8373 (mmm-85) REVERT: E 47 ARG cc_start: 0.7001 (mtt-85) cc_final: 0.6476 (ttm110) REVERT: E 63 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7748 (mp0) REVERT: E 67 LYS cc_start: 0.7868 (mttm) cc_final: 0.7535 (mptt) REVERT: R 121 VAL cc_start: 0.8647 (p) cc_final: 0.8405 (p) REVERT: R 126 LYS cc_start: 0.8536 (ttmm) cc_final: 0.8328 (ttmm) REVERT: R 127 GLU cc_start: 0.8844 (tp30) cc_final: 0.8018 (tp30) REVERT: R 224 LEU cc_start: 0.8889 (tp) cc_final: 0.8596 (tp) REVERT: R 227 MET cc_start: 0.7898 (mtp) cc_final: 0.7623 (ttm) REVERT: R 228 LEU cc_start: 0.9174 (mm) cc_final: 0.8824 (mm) REVERT: R 287 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7991 (pp20) REVERT: R 300 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: R 306 HIS cc_start: 0.8371 (OUTLIER) cc_final: 0.8023 (t70) REVERT: R 314 TYR cc_start: 0.8897 (m-80) cc_final: 0.8532 (m-80) REVERT: R 323 HIS cc_start: 0.8245 (m90) cc_final: 0.7929 (m-70) REVERT: S 95 TYR cc_start: 0.8783 (m-10) cc_final: 0.8510 (m-10) REVERT: S 97 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8829 (m) REVERT: S 164 TRP cc_start: 0.8998 (m100) cc_final: 0.8700 (m100) REVERT: S 219 GLN cc_start: 0.8953 (pp30) cc_final: 0.8618 (pp30) REVERT: S 222 GLU cc_start: 0.7615 (tp30) cc_final: 0.7175 (tp30) outliers start: 41 outliers final: 26 residues processed: 324 average time/residue: 0.2352 time to fit residues: 103.5047 Evaluate side-chains 303 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 272 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 300 GLU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 124 optimal weight: 0.2980 chunk 102 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS S 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10390 Z= 0.248 Angle : 0.634 8.598 14079 Z= 0.327 Chirality : 0.043 0.171 1621 Planarity : 0.005 0.070 1768 Dihedral : 5.838 39.461 1474 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.74 % Allowed : 20.42 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.21), residues: 1284 helix: -1.83 (0.22), residues: 420 sheet: -2.87 (0.26), residues: 300 loop : -2.38 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 112 HIS 0.002 0.001 HIS R 247 PHE 0.015 0.001 PHE R 218 TYR 0.027 0.001 TYR A 302 ARG 0.004 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 301 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8852 (t70) cc_final: 0.8512 (t0) REVERT: A 29 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8186 (tppt) REVERT: A 243 MET cc_start: 0.8832 (tpp) cc_final: 0.8343 (tpp) REVERT: A 302 TYR cc_start: 0.8801 (t80) cc_final: 0.8360 (t80) REVERT: A 341 ASP cc_start: 0.8598 (t0) cc_final: 0.8241 (t0) REVERT: A 346 ASN cc_start: 0.9153 (m-40) cc_final: 0.8850 (m110) REVERT: A 349 LYS cc_start: 0.8983 (tttm) cc_final: 0.8709 (ttpp) REVERT: B 13 GLN cc_start: 0.8922 (mm110) cc_final: 0.7638 (tm-30) REVERT: B 105 TYR cc_start: 0.9080 (t80) cc_final: 0.8499 (t80) REVERT: B 157 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8876 (tt) REVERT: B 172 GLU cc_start: 0.8001 (mp0) cc_final: 0.7773 (mm-30) REVERT: B 188 MET cc_start: 0.8124 (mmm) cc_final: 0.7876 (mmm) REVERT: B 211 TRP cc_start: 0.9098 (m100) cc_final: 0.8372 (m100) REVERT: B 234 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8614 (m-80) REVERT: B 259 GLN cc_start: 0.7967 (pt0) cc_final: 0.7393 (pt0) REVERT: C 13 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.8187 (ptp-110) REVERT: C 20 LYS cc_start: 0.8803 (mttp) cc_final: 0.8595 (ttmm) REVERT: C 25 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8610 (mp) REVERT: C 38 MET cc_start: 0.7749 (ppp) cc_final: 0.7172 (ppp) REVERT: D 4 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8008 (mm-30) REVERT: D 6 ARG cc_start: 0.8683 (ttp-170) cc_final: 0.8293 (ptm160) REVERT: D 13 TYR cc_start: 0.7931 (t80) cc_final: 0.7691 (t80) REVERT: D 23 LYS cc_start: 0.7788 (ttmt) cc_final: 0.7586 (tttt) REVERT: D 29 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7007 (tm-30) REVERT: D 47 ARG cc_start: 0.7909 (ppt170) cc_final: 0.7681 (ppt170) REVERT: D 68 ARG cc_start: 0.8612 (mmm160) cc_final: 0.8200 (mmm-85) REVERT: E 47 ARG cc_start: 0.6872 (mtt-85) cc_final: 0.6408 (ttm110) REVERT: R 121 VAL cc_start: 0.8684 (p) cc_final: 0.8474 (p) REVERT: R 126 LYS cc_start: 0.8561 (ttmm) cc_final: 0.8206 (ttpp) REVERT: R 143 ASP cc_start: 0.8845 (t70) cc_final: 0.8632 (t0) REVERT: R 163 LYS cc_start: 0.8150 (mppt) cc_final: 0.7572 (mptt) REVERT: R 224 LEU cc_start: 0.8838 (tp) cc_final: 0.8577 (tp) REVERT: R 227 MET cc_start: 0.7838 (mtp) cc_final: 0.7570 (ttm) REVERT: R 228 LEU cc_start: 0.9158 (mm) cc_final: 0.8812 (mm) REVERT: R 287 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8028 (pp20) REVERT: R 300 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7475 (tt0) REVERT: R 306 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.8036 (t70) REVERT: R 314 TYR cc_start: 0.8895 (m-80) cc_final: 0.8436 (m-80) REVERT: R 323 HIS cc_start: 0.8326 (m90) cc_final: 0.7935 (m-70) REVERT: S 6 GLU cc_start: 0.7629 (pm20) cc_final: 0.6049 (pm20) REVERT: S 95 TYR cc_start: 0.8647 (m-10) cc_final: 0.8392 (m-10) REVERT: S 128 MET cc_start: 0.8814 (mmm) cc_final: 0.8134 (mmm) REVERT: S 130 GLN cc_start: 0.7540 (mt0) cc_final: 0.7166 (mt0) REVERT: S 164 TRP cc_start: 0.8976 (m100) cc_final: 0.8642 (m100) REVERT: S 210 GLU cc_start: 0.7767 (tp30) cc_final: 0.7289 (mm-30) REVERT: S 219 GLN cc_start: 0.8959 (pp30) cc_final: 0.8552 (pp30) REVERT: S 221 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9034 (mt) REVERT: S 222 GLU cc_start: 0.7481 (tp30) cc_final: 0.7000 (tp30) outliers start: 52 outliers final: 34 residues processed: 327 average time/residue: 0.2349 time to fit residues: 104.6274 Evaluate side-chains 321 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 282 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS R 66 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS S 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10390 Z= 0.178 Angle : 0.603 9.261 14079 Z= 0.306 Chirality : 0.042 0.177 1621 Planarity : 0.004 0.067 1768 Dihedral : 5.372 37.317 1474 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.47 % Allowed : 22.33 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.22), residues: 1284 helix: -1.28 (0.24), residues: 428 sheet: -2.69 (0.26), residues: 315 loop : -2.29 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 112 HIS 0.004 0.001 HIS S 35 PHE 0.023 0.001 PHE S 68 TYR 0.024 0.001 TYR A 302 ARG 0.009 0.000 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 309 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8866 (t70) cc_final: 0.8590 (t0) REVERT: A 29 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8380 (ttmt) REVERT: A 243 MET cc_start: 0.8777 (tpp) cc_final: 0.8369 (tpp) REVERT: A 318 GLU cc_start: 0.7558 (mp0) cc_final: 0.7349 (mp0) REVERT: A 341 ASP cc_start: 0.8517 (t0) cc_final: 0.8230 (t0) REVERT: A 349 LYS cc_start: 0.8963 (tttm) cc_final: 0.8681 (ttpp) REVERT: B 13 GLN cc_start: 0.8861 (mm110) cc_final: 0.7791 (tm-30) REVERT: B 82 TRP cc_start: 0.8878 (m100) cc_final: 0.8183 (m100) REVERT: B 105 TYR cc_start: 0.9039 (t80) cc_final: 0.8619 (t80) REVERT: B 188 MET cc_start: 0.8168 (mmm) cc_final: 0.7905 (mmm) REVERT: B 211 TRP cc_start: 0.9100 (m100) cc_final: 0.8522 (m100) REVERT: B 234 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8605 (m-80) REVERT: B 252 LEU cc_start: 0.9169 (tt) cc_final: 0.8763 (tp) REVERT: B 258 ASP cc_start: 0.7851 (t0) cc_final: 0.7083 (t0) REVERT: B 259 GLN cc_start: 0.7759 (pt0) cc_final: 0.7540 (pt0) REVERT: C 13 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.8236 (ptp-110) REVERT: C 25 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8682 (mp) REVERT: D 6 ARG cc_start: 0.8645 (ttp-170) cc_final: 0.8233 (ptm160) REVERT: D 29 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7014 (tm-30) REVERT: D 47 ARG cc_start: 0.7756 (ppt170) cc_final: 0.7547 (ppt170) REVERT: D 68 ARG cc_start: 0.8683 (mmm160) cc_final: 0.8176 (mmm-85) REVERT: E 47 ARG cc_start: 0.6755 (mtt-85) cc_final: 0.6333 (ttm110) REVERT: R 59 PHE cc_start: 0.8347 (t80) cc_final: 0.8125 (t80) REVERT: R 86 TYR cc_start: 0.8252 (m-10) cc_final: 0.7748 (m-10) REVERT: R 126 LYS cc_start: 0.8484 (ttmm) cc_final: 0.8048 (ttpp) REVERT: R 131 TYR cc_start: 0.8671 (m-80) cc_final: 0.8366 (m-80) REVERT: R 163 LYS cc_start: 0.8189 (mppt) cc_final: 0.7627 (mptt) REVERT: R 224 LEU cc_start: 0.8781 (tp) cc_final: 0.8484 (tp) REVERT: R 227 MET cc_start: 0.7769 (mtp) cc_final: 0.7445 (ttm) REVERT: R 228 LEU cc_start: 0.9118 (mm) cc_final: 0.8825 (mm) REVERT: R 287 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8036 (pp20) REVERT: R 300 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7371 (tt0) REVERT: R 306 HIS cc_start: 0.8024 (OUTLIER) cc_final: 0.7665 (t70) REVERT: R 323 HIS cc_start: 0.8318 (m90) cc_final: 0.7954 (m-70) REVERT: S 128 MET cc_start: 0.8748 (mmm) cc_final: 0.8306 (mmm) REVERT: S 130 GLN cc_start: 0.7577 (mt0) cc_final: 0.7112 (mt0) REVERT: S 164 TRP cc_start: 0.8925 (m100) cc_final: 0.8629 (m100) REVERT: S 210 GLU cc_start: 0.7811 (tp30) cc_final: 0.7405 (mm-30) REVERT: S 219 GLN cc_start: 0.8902 (pp30) cc_final: 0.8494 (pp30) outliers start: 49 outliers final: 32 residues processed: 332 average time/residue: 0.2340 time to fit residues: 105.3999 Evaluate side-chains 317 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 281 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 300 GLU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.0000 chunk 69 optimal weight: 30.0000 chunk 1 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 110 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN R 66 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS R 247 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10390 Z= 0.234 Angle : 0.617 9.663 14079 Z= 0.313 Chirality : 0.043 0.151 1621 Planarity : 0.004 0.067 1768 Dihedral : 5.313 37.291 1474 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.10 % Allowed : 23.34 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.23), residues: 1284 helix: -0.95 (0.25), residues: 430 sheet: -2.54 (0.27), residues: 317 loop : -2.20 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 112 HIS 0.002 0.001 HIS A 213 PHE 0.019 0.001 PHE S 200 TYR 0.027 0.001 TYR A 302 ARG 0.005 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 287 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8899 (t70) cc_final: 0.8537 (t0) REVERT: A 29 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8150 (tppt) REVERT: A 243 MET cc_start: 0.8775 (tpp) cc_final: 0.8369 (tpp) REVERT: A 341 ASP cc_start: 0.8584 (t0) cc_final: 0.8303 (t0) REVERT: A 349 LYS cc_start: 0.8973 (tttm) cc_final: 0.8690 (ttpp) REVERT: B 13 GLN cc_start: 0.8857 (mm110) cc_final: 0.7737 (tm-30) REVERT: B 82 TRP cc_start: 0.8904 (m100) cc_final: 0.8229 (m100) REVERT: B 105 TYR cc_start: 0.9059 (t80) cc_final: 0.8566 (t80) REVERT: B 188 MET cc_start: 0.8223 (mmm) cc_final: 0.7972 (mmm) REVERT: B 228 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7838 (p0) REVERT: B 229 ILE cc_start: 0.8857 (mt) cc_final: 0.8602 (mt) REVERT: B 234 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: B 258 ASP cc_start: 0.7937 (t0) cc_final: 0.7139 (t0) REVERT: B 259 GLN cc_start: 0.7708 (pt0) cc_final: 0.7151 (pt0) REVERT: B 261 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8892 (mm) REVERT: C 13 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.8301 (ptp-110) REVERT: C 25 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8705 (mp) REVERT: D 4 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8062 (mm-30) REVERT: D 29 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6979 (tm-30) REVERT: D 47 ARG cc_start: 0.7772 (ppt170) cc_final: 0.7520 (ppt170) REVERT: D 68 ARG cc_start: 0.8554 (mmm160) cc_final: 0.8026 (mmm-85) REVERT: E 47 ARG cc_start: 0.6814 (mtt-85) cc_final: 0.6378 (ttm110) REVERT: R 86 TYR cc_start: 0.8244 (m-10) cc_final: 0.7786 (m-10) REVERT: R 126 LYS cc_start: 0.8480 (ttmm) cc_final: 0.8076 (ttpp) REVERT: R 127 GLU cc_start: 0.8721 (tp30) cc_final: 0.7922 (tp30) REVERT: R 131 TYR cc_start: 0.8624 (m-80) cc_final: 0.8233 (m-80) REVERT: R 209 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7682 (mpp) REVERT: R 224 LEU cc_start: 0.8825 (tp) cc_final: 0.8538 (tp) REVERT: R 227 MET cc_start: 0.7808 (mtp) cc_final: 0.7489 (ttm) REVERT: R 228 LEU cc_start: 0.9117 (mm) cc_final: 0.8823 (mm) REVERT: R 287 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8032 (pp20) REVERT: R 300 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: R 306 HIS cc_start: 0.8118 (OUTLIER) cc_final: 0.7773 (t70) REVERT: R 314 TYR cc_start: 0.8763 (m-80) cc_final: 0.8241 (m-80) REVERT: R 323 HIS cc_start: 0.8336 (m90) cc_final: 0.7882 (m170) REVERT: S 128 MET cc_start: 0.8737 (mmm) cc_final: 0.8236 (mmm) REVERT: S 130 GLN cc_start: 0.7499 (mt0) cc_final: 0.7027 (mt0) REVERT: S 164 TRP cc_start: 0.8944 (m100) cc_final: 0.8627 (m100) REVERT: S 219 GLN cc_start: 0.8972 (pp30) cc_final: 0.8508 (pp30) outliers start: 56 outliers final: 39 residues processed: 317 average time/residue: 0.2235 time to fit residues: 96.8477 Evaluate side-chains 323 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 277 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 209 MET Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 300 GLU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 0.0370 chunk 64 optimal weight: 0.9980 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS R 247 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10390 Z= 0.169 Angle : 0.591 9.867 14079 Z= 0.299 Chirality : 0.042 0.157 1621 Planarity : 0.004 0.068 1768 Dihedral : 5.041 36.063 1474 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.01 % Allowed : 23.43 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.23), residues: 1284 helix: -0.57 (0.26), residues: 421 sheet: -2.38 (0.27), residues: 305 loop : -2.03 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 112 HIS 0.003 0.000 HIS S 35 PHE 0.019 0.001 PHE S 200 TYR 0.022 0.001 TYR A 302 ARG 0.006 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 287 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8899 (t70) cc_final: 0.8531 (t0) REVERT: A 29 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8352 (ttmt) REVERT: A 243 MET cc_start: 0.8751 (tpp) cc_final: 0.8357 (tpp) REVERT: A 341 ASP cc_start: 0.8522 (t0) cc_final: 0.8270 (t0) REVERT: A 349 LYS cc_start: 0.8930 (tttm) cc_final: 0.8670 (ttpp) REVERT: B 82 TRP cc_start: 0.8891 (m100) cc_final: 0.8293 (m100) REVERT: B 101 MET cc_start: 0.8876 (mtp) cc_final: 0.8517 (mtp) REVERT: B 105 TYR cc_start: 0.9034 (t80) cc_final: 0.8649 (t80) REVERT: B 157 ILE cc_start: 0.8820 (tt) cc_final: 0.8473 (tt) REVERT: B 188 MET cc_start: 0.8220 (mmm) cc_final: 0.7937 (mmm) REVERT: B 211 TRP cc_start: 0.9116 (m100) cc_final: 0.8373 (m100) REVERT: B 229 ILE cc_start: 0.8753 (mt) cc_final: 0.8502 (mt) REVERT: B 234 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: B 258 ASP cc_start: 0.7899 (t0) cc_final: 0.7183 (t0) REVERT: B 259 GLN cc_start: 0.7599 (pt0) cc_final: 0.7133 (pt0) REVERT: B 261 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8841 (mm) REVERT: B 332 TRP cc_start: 0.8753 (m-10) cc_final: 0.8469 (m-10) REVERT: C 13 ARG cc_start: 0.8651 (ttm-80) cc_final: 0.8337 (ptp-110) REVERT: C 25 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8654 (mp) REVERT: C 32 LYS cc_start: 0.8908 (ttmt) cc_final: 0.8657 (ttpp) REVERT: D 6 ARG cc_start: 0.8742 (ttp-170) cc_final: 0.8266 (ptm160) REVERT: D 23 LYS cc_start: 0.7808 (tttt) cc_final: 0.7473 (ttmt) REVERT: D 29 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6778 (tm-30) REVERT: E 47 ARG cc_start: 0.6711 (mtt-85) cc_final: 0.6307 (ttm110) REVERT: E 60 ARG cc_start: 0.8087 (mmm160) cc_final: 0.7510 (mmm160) REVERT: R 86 TYR cc_start: 0.8190 (m-10) cc_final: 0.7665 (m-10) REVERT: R 126 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8027 (ttpp) REVERT: R 127 GLU cc_start: 0.8783 (tp30) cc_final: 0.8507 (tp30) REVERT: R 224 LEU cc_start: 0.8759 (tp) cc_final: 0.8431 (tp) REVERT: R 227 MET cc_start: 0.7695 (mtp) cc_final: 0.7422 (ttm) REVERT: R 228 LEU cc_start: 0.9006 (mm) cc_final: 0.8711 (mm) REVERT: R 287 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7843 (pp20) REVERT: R 300 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: R 306 HIS cc_start: 0.8004 (OUTLIER) cc_final: 0.7596 (t70) REVERT: R 323 HIS cc_start: 0.8322 (m90) cc_final: 0.7872 (m170) REVERT: R 327 LYS cc_start: 0.8450 (mtpt) cc_final: 0.8071 (ptmt) REVERT: S 128 MET cc_start: 0.8653 (mmm) cc_final: 0.8133 (mmm) REVERT: S 130 GLN cc_start: 0.7631 (mt0) cc_final: 0.7368 (mt0) REVERT: S 164 TRP cc_start: 0.8920 (m100) cc_final: 0.8618 (m100) REVERT: S 167 GLN cc_start: 0.8560 (tt0) cc_final: 0.8305 (tt0) REVERT: S 219 GLN cc_start: 0.8897 (pp30) cc_final: 0.8634 (pp30) outliers start: 55 outliers final: 36 residues processed: 316 average time/residue: 0.2254 time to fit residues: 98.3446 Evaluate side-chains 319 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 278 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 300 GLU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN D 8 GLN R 66 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10390 Z= 0.237 Angle : 0.632 9.917 14079 Z= 0.317 Chirality : 0.042 0.159 1621 Planarity : 0.004 0.076 1768 Dihedral : 5.103 35.766 1474 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 5.20 % Allowed : 24.52 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.23), residues: 1284 helix: -0.27 (0.26), residues: 412 sheet: -2.40 (0.27), residues: 312 loop : -1.96 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 112 HIS 0.003 0.001 HIS A 188 PHE 0.019 0.001 PHE S 200 TYR 0.020 0.001 TYR B 59 ARG 0.007 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 279 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8877 (t70) cc_final: 0.8506 (t0) REVERT: A 29 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8355 (tppt) REVERT: A 243 MET cc_start: 0.8780 (tpp) cc_final: 0.8371 (tpp) REVERT: A 341 ASP cc_start: 0.8588 (t0) cc_final: 0.8320 (t0) REVERT: A 349 LYS cc_start: 0.8932 (tttm) cc_final: 0.8696 (ttpp) REVERT: B 82 TRP cc_start: 0.8903 (m100) cc_final: 0.8261 (m100) REVERT: B 101 MET cc_start: 0.8942 (mtp) cc_final: 0.8567 (mtp) REVERT: B 105 TYR cc_start: 0.9058 (t80) cc_final: 0.8580 (t80) REVERT: B 157 ILE cc_start: 0.8918 (tt) cc_final: 0.8578 (tt) REVERT: B 188 MET cc_start: 0.8236 (mmm) cc_final: 0.7978 (mmm) REVERT: B 211 TRP cc_start: 0.9109 (m100) cc_final: 0.8495 (m100) REVERT: B 229 ILE cc_start: 0.8813 (mt) cc_final: 0.8547 (mt) REVERT: B 234 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8723 (m-80) REVERT: B 258 ASP cc_start: 0.8047 (t0) cc_final: 0.7288 (t0) REVERT: B 259 GLN cc_start: 0.7720 (pt0) cc_final: 0.7259 (pt0) REVERT: B 261 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8912 (mm) REVERT: B 284 LEU cc_start: 0.9121 (mp) cc_final: 0.8853 (tp) REVERT: C 13 ARG cc_start: 0.8682 (ttm-80) cc_final: 0.8358 (ptp-110) REVERT: C 25 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8700 (mp) REVERT: D 6 ARG cc_start: 0.8726 (ttp-170) cc_final: 0.8344 (ptm160) REVERT: D 23 LYS cc_start: 0.7775 (tttt) cc_final: 0.7350 (ttmt) REVERT: D 27 VAL cc_start: 0.9304 (t) cc_final: 0.9039 (p) REVERT: D 29 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6872 (tm-30) REVERT: E 47 ARG cc_start: 0.6798 (mtt-85) cc_final: 0.6360 (ttm110) REVERT: R 86 TYR cc_start: 0.8206 (m-10) cc_final: 0.7669 (m-10) REVERT: R 126 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8146 (ttpp) REVERT: R 224 LEU cc_start: 0.8826 (tp) cc_final: 0.8526 (tp) REVERT: R 227 MET cc_start: 0.7800 (mtp) cc_final: 0.7470 (ttm) REVERT: R 228 LEU cc_start: 0.9023 (mm) cc_final: 0.8710 (mm) REVERT: R 264 TRP cc_start: 0.8344 (m100) cc_final: 0.8094 (m100) REVERT: R 287 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7827 (pp20) REVERT: R 306 HIS cc_start: 0.8023 (OUTLIER) cc_final: 0.7603 (t70) REVERT: R 323 HIS cc_start: 0.8350 (m90) cc_final: 0.7845 (m170) REVERT: S 128 MET cc_start: 0.8724 (mmm) cc_final: 0.8179 (mmm) REVERT: S 130 GLN cc_start: 0.7587 (mt0) cc_final: 0.7245 (mt0) REVERT: S 167 GLN cc_start: 0.8554 (tt0) cc_final: 0.8298 (tt0) REVERT: S 219 GLN cc_start: 0.8974 (pp30) cc_final: 0.8282 (pp30) REVERT: S 221 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8926 (mt) outliers start: 57 outliers final: 45 residues processed: 309 average time/residue: 0.2396 time to fit residues: 102.7331 Evaluate side-chains 316 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 266 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN R 66 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10390 Z= 0.189 Angle : 0.631 10.446 14079 Z= 0.313 Chirality : 0.042 0.154 1621 Planarity : 0.004 0.074 1768 Dihedral : 4.941 35.697 1474 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.01 % Allowed : 24.70 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.23), residues: 1284 helix: -0.18 (0.26), residues: 418 sheet: -2.38 (0.27), residues: 303 loop : -1.90 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 332 HIS 0.004 0.001 HIS A 188 PHE 0.018 0.001 PHE S 200 TYR 0.017 0.001 TYR B 59 ARG 0.007 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 280 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8942 (t70) cc_final: 0.8564 (t0) REVERT: A 29 LYS cc_start: 0.8745 (ttmm) cc_final: 0.8391 (tppt) REVERT: A 240 MET cc_start: 0.7651 (pmm) cc_final: 0.7397 (pmm) REVERT: A 243 MET cc_start: 0.8765 (tpp) cc_final: 0.8369 (tpp) REVERT: A 255 ASN cc_start: 0.8277 (m-40) cc_final: 0.7944 (m-40) REVERT: A 341 ASP cc_start: 0.8533 (t0) cc_final: 0.8321 (t0) REVERT: B 82 TRP cc_start: 0.8878 (m100) cc_final: 0.8283 (m100) REVERT: B 101 MET cc_start: 0.8930 (mtp) cc_final: 0.8601 (mtp) REVERT: B 105 TYR cc_start: 0.9041 (t80) cc_final: 0.8570 (t80) REVERT: B 157 ILE cc_start: 0.8877 (tt) cc_final: 0.8499 (tt) REVERT: B 211 TRP cc_start: 0.9137 (m100) cc_final: 0.8484 (m100) REVERT: B 234 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8674 (m-80) REVERT: B 252 LEU cc_start: 0.9179 (tt) cc_final: 0.8961 (tp) REVERT: B 258 ASP cc_start: 0.8103 (t0) cc_final: 0.7439 (t0) REVERT: B 259 GLN cc_start: 0.7590 (pt0) cc_final: 0.7125 (pm20) REVERT: B 284 LEU cc_start: 0.9095 (mp) cc_final: 0.8846 (tp) REVERT: C 13 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8356 (ptp-110) REVERT: C 25 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8434 (mp) REVERT: C 62 ARG cc_start: 0.7844 (ttm110) cc_final: 0.7499 (ttm110) REVERT: D 6 ARG cc_start: 0.8692 (ttp-170) cc_final: 0.8244 (ptm160) REVERT: D 23 LYS cc_start: 0.7888 (tttt) cc_final: 0.7556 (ttmt) REVERT: D 27 VAL cc_start: 0.9320 (t) cc_final: 0.9047 (p) REVERT: D 29 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6859 (tm-30) REVERT: E 47 ARG cc_start: 0.6670 (mtt-85) cc_final: 0.6315 (ttm110) REVERT: R 86 TYR cc_start: 0.8164 (m-10) cc_final: 0.7647 (m-10) REVERT: R 126 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8101 (ttpp) REVERT: R 127 GLU cc_start: 0.8743 (tp30) cc_final: 0.8131 (tp30) REVERT: R 224 LEU cc_start: 0.8718 (tp) cc_final: 0.8380 (tp) REVERT: R 227 MET cc_start: 0.7778 (mtp) cc_final: 0.7455 (ttm) REVERT: R 228 LEU cc_start: 0.8986 (mm) cc_final: 0.8686 (mm) REVERT: R 229 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7161 (m-10) REVERT: R 264 TRP cc_start: 0.8289 (m100) cc_final: 0.8074 (m100) REVERT: R 287 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7830 (pp20) REVERT: R 306 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7486 (t70) REVERT: R 323 HIS cc_start: 0.8340 (m90) cc_final: 0.7845 (m170) REVERT: R 327 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8174 (ptmt) REVERT: S 128 MET cc_start: 0.8671 (mmm) cc_final: 0.8123 (mmm) REVERT: S 130 GLN cc_start: 0.7563 (mt0) cc_final: 0.7196 (mt0) REVERT: S 164 TRP cc_start: 0.8934 (m100) cc_final: 0.8614 (m100) REVERT: S 219 GLN cc_start: 0.8905 (pp30) cc_final: 0.8462 (pp30) outliers start: 55 outliers final: 43 residues processed: 310 average time/residue: 0.2357 time to fit residues: 99.4482 Evaluate side-chains 311 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 264 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 68 optimal weight: 30.0000 chunk 49 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN D 8 GLN R 66 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10390 Z= 0.187 Angle : 0.638 10.664 14079 Z= 0.317 Chirality : 0.042 0.158 1621 Planarity : 0.004 0.073 1768 Dihedral : 4.844 35.911 1474 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.65 % Allowed : 25.89 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.23), residues: 1284 helix: -0.09 (0.26), residues: 423 sheet: -2.32 (0.28), residues: 290 loop : -1.78 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 332 HIS 0.004 0.001 HIS S 35 PHE 0.018 0.001 PHE R 218 TYR 0.015 0.001 TYR B 59 ARG 0.006 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 282 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8909 (t70) cc_final: 0.8514 (t0) REVERT: A 29 LYS cc_start: 0.8737 (ttmm) cc_final: 0.8400 (tppt) REVERT: A 243 MET cc_start: 0.8765 (tpp) cc_final: 0.8365 (tpp) REVERT: A 255 ASN cc_start: 0.8257 (m-40) cc_final: 0.8005 (m-40) REVERT: A 305 CYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7714 (m) REVERT: A 306 GLN cc_start: 0.8767 (tp40) cc_final: 0.8281 (tt0) REVERT: A 341 ASP cc_start: 0.8531 (t0) cc_final: 0.8323 (t0) REVERT: B 82 TRP cc_start: 0.8886 (m100) cc_final: 0.8585 (m100) REVERT: B 101 MET cc_start: 0.8975 (mtp) cc_final: 0.8658 (mtp) REVERT: B 105 TYR cc_start: 0.9049 (t80) cc_final: 0.8607 (t80) REVERT: B 157 ILE cc_start: 0.8881 (tt) cc_final: 0.8523 (tt) REVERT: B 211 TRP cc_start: 0.9136 (m100) cc_final: 0.8469 (m100) REVERT: B 258 ASP cc_start: 0.8027 (t0) cc_final: 0.7411 (t0) REVERT: B 259 GLN cc_start: 0.7492 (pt0) cc_final: 0.7062 (pt0) REVERT: C 13 ARG cc_start: 0.8663 (ttm-80) cc_final: 0.8349 (ptp-110) REVERT: C 25 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8381 (mp) REVERT: D 6 ARG cc_start: 0.8688 (ttp-170) cc_final: 0.8267 (ptm160) REVERT: D 23 LYS cc_start: 0.7854 (tttt) cc_final: 0.7539 (ttmt) REVERT: D 27 VAL cc_start: 0.9282 (t) cc_final: 0.8971 (p) REVERT: D 29 GLU cc_start: 0.7372 (tm-30) cc_final: 0.6843 (tm-30) REVERT: E 47 ARG cc_start: 0.6650 (mtt-85) cc_final: 0.6302 (ttm110) REVERT: E 63 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7629 (mt-10) REVERT: R 50 PHE cc_start: 0.7863 (m-10) cc_final: 0.7586 (m-10) REVERT: R 86 TYR cc_start: 0.8133 (m-10) cc_final: 0.7622 (m-10) REVERT: R 114 PHE cc_start: 0.4265 (m-10) cc_final: 0.3841 (m-80) REVERT: R 126 LYS cc_start: 0.8399 (ttmm) cc_final: 0.8099 (ttpp) REVERT: R 127 GLU cc_start: 0.8732 (tp30) cc_final: 0.8317 (tp30) REVERT: R 224 LEU cc_start: 0.8702 (tp) cc_final: 0.8360 (tp) REVERT: R 227 MET cc_start: 0.7800 (mtp) cc_final: 0.7466 (ttm) REVERT: R 228 LEU cc_start: 0.8965 (mm) cc_final: 0.8676 (mm) REVERT: R 229 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7170 (m-10) REVERT: R 287 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7813 (pp20) REVERT: R 306 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7237 (t70) REVERT: R 323 HIS cc_start: 0.8344 (m90) cc_final: 0.7838 (m170) REVERT: R 327 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8189 (ptmt) REVERT: S 128 MET cc_start: 0.8677 (mmm) cc_final: 0.8114 (mmm) REVERT: S 130 GLN cc_start: 0.7671 (mt0) cc_final: 0.7300 (mt0) REVERT: S 164 TRP cc_start: 0.8927 (m100) cc_final: 0.8595 (m100) REVERT: S 167 GLN cc_start: 0.8404 (tt0) cc_final: 0.8167 (tt0) REVERT: S 219 GLN cc_start: 0.8908 (pp30) cc_final: 0.8462 (pp30) outliers start: 51 outliers final: 40 residues processed: 309 average time/residue: 0.2381 time to fit residues: 100.0773 Evaluate side-chains 310 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 266 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 6.9990 chunk 120 optimal weight: 0.0040 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 77 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 overall best weight: 1.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN R 66 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10390 Z= 0.264 Angle : 0.683 11.451 14079 Z= 0.340 Chirality : 0.043 0.162 1621 Planarity : 0.004 0.073 1768 Dihedral : 5.034 36.671 1474 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.56 % Allowed : 26.44 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.23), residues: 1284 helix: 0.02 (0.26), residues: 421 sheet: -2.30 (0.28), residues: 293 loop : -1.78 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 112 HIS 0.004 0.001 HIS B 54 PHE 0.017 0.001 PHE R 218 TYR 0.020 0.001 TYR B 59 ARG 0.010 0.000 ARG B 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 271 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8614 (m-30) cc_final: 0.8299 (m-30) REVERT: A 26 ASP cc_start: 0.8949 (t70) cc_final: 0.8521 (t0) REVERT: A 29 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8415 (tppt) REVERT: A 240 MET cc_start: 0.7488 (pmm) cc_final: 0.7246 (pmm) REVERT: A 243 MET cc_start: 0.8787 (tpp) cc_final: 0.8397 (tpp) REVERT: A 255 ASN cc_start: 0.8256 (m-40) cc_final: 0.7900 (m-40) REVERT: A 305 CYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7774 (m) REVERT: A 306 GLN cc_start: 0.8832 (tp40) cc_final: 0.8364 (tt0) REVERT: A 341 ASP cc_start: 0.8602 (t0) cc_final: 0.8327 (t0) REVERT: B 82 TRP cc_start: 0.8759 (m100) cc_final: 0.8477 (m100) REVERT: B 101 MET cc_start: 0.8991 (mtp) cc_final: 0.8676 (mtp) REVERT: B 105 TYR cc_start: 0.9063 (t80) cc_final: 0.8549 (t80) REVERT: B 157 ILE cc_start: 0.9006 (tt) cc_final: 0.8666 (tt) REVERT: B 228 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8036 (p0) REVERT: B 258 ASP cc_start: 0.8271 (t0) cc_final: 0.7600 (t0) REVERT: B 259 GLN cc_start: 0.7915 (pt0) cc_final: 0.7378 (pt0) REVERT: C 13 ARG cc_start: 0.8613 (ttm-80) cc_final: 0.8340 (ptp-110) REVERT: C 25 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8465 (mp) REVERT: C 62 ARG cc_start: 0.7936 (ttm110) cc_final: 0.7589 (ttm110) REVERT: D 23 LYS cc_start: 0.7908 (tttt) cc_final: 0.7482 (ttmt) REVERT: D 27 VAL cc_start: 0.9307 (t) cc_final: 0.8989 (p) REVERT: D 29 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6861 (tm-30) REVERT: E 47 ARG cc_start: 0.6629 (mtt-85) cc_final: 0.6239 (ttm110) REVERT: E 63 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7611 (mt-10) REVERT: R 86 TYR cc_start: 0.8179 (m-10) cc_final: 0.7641 (m-10) REVERT: R 126 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8127 (ttpp) REVERT: R 127 GLU cc_start: 0.8748 (tp30) cc_final: 0.8328 (tp30) REVERT: R 224 LEU cc_start: 0.8821 (tp) cc_final: 0.8527 (tp) REVERT: R 227 MET cc_start: 0.7751 (mtp) cc_final: 0.7484 (ttm) REVERT: R 228 LEU cc_start: 0.9005 (mm) cc_final: 0.8690 (mm) REVERT: R 229 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7258 (m-10) REVERT: R 264 TRP cc_start: 0.8329 (m100) cc_final: 0.8110 (m100) REVERT: R 287 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7812 (pp20) REVERT: R 304 ILE cc_start: 0.9191 (tp) cc_final: 0.8955 (tp) REVERT: R 306 HIS cc_start: 0.7604 (OUTLIER) cc_final: 0.7229 (t70) REVERT: R 323 HIS cc_start: 0.8378 (m90) cc_final: 0.7829 (m170) REVERT: S 128 MET cc_start: 0.8745 (mmm) cc_final: 0.8178 (mmm) REVERT: S 130 GLN cc_start: 0.7599 (mt0) cc_final: 0.7256 (mt0) REVERT: S 167 GLN cc_start: 0.8436 (tt0) cc_final: 0.8204 (tt0) REVERT: S 219 GLN cc_start: 0.8992 (pp30) cc_final: 0.8777 (pp30) outliers start: 50 outliers final: 36 residues processed: 297 average time/residue: 0.2452 time to fit residues: 99.7662 Evaluate side-chains 304 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 263 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN D 8 GLN R 66 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.146332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.115181 restraints weight = 17036.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.118316 restraints weight = 8610.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.119297 restraints weight = 5467.331| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10390 Z= 0.187 Angle : 0.658 11.759 14079 Z= 0.321 Chirality : 0.042 0.155 1621 Planarity : 0.004 0.072 1768 Dihedral : 4.881 36.342 1474 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.92 % Allowed : 27.16 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.24), residues: 1284 helix: 0.23 (0.27), residues: 417 sheet: -2.26 (0.27), residues: 290 loop : -1.73 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 112 HIS 0.004 0.001 HIS S 35 PHE 0.018 0.001 PHE R 218 TYR 0.016 0.001 TYR B 59 ARG 0.008 0.000 ARG C 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2543.15 seconds wall clock time: 46 minutes 30.03 seconds (2790.03 seconds total)