Starting phenix.real_space_refine on Fri Nov 15 07:54:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/11_2024/8id3_35356.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/11_2024/8id3_35356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/11_2024/8id3_35356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/11_2024/8id3_35356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/11_2024/8id3_35356.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/11_2024/8id3_35356.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5585 2.51 5 N 1492 2.21 5 O 1607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8742 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2566 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "S" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1752 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "Y" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 432 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1762 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "R" Number of atoms: 2209 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 291, 2198 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 70 Conformer: "B" Number of residues, atoms: 291, 2198 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 70 bond proxies already assigned to first conformer: 2234 Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'7NR': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG R 261 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG R 261 " occ=0.50 Time building chain proxies: 6.21, per 1000 atoms: 0.71 Number of scatterers: 8742 At special positions: 0 Unit cell: (107.484, 126.75, 117.624, 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 58 16.00 O 1607 8.00 N 1492 7.00 C 5585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.36 Conformation dependent library (CDL) restraints added in 1.4 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 35.8% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.640A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 221 through 225 removed outlier: 4.051A pdb=" N VAL S 225 " --> pdb=" O ALA S 222 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 23 Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.634A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.805A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.911A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.057A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'R' and resid 37 through 68 Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.530A pdb=" N ASN R 80 " --> pdb=" O CYS R 76 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 109 through 142 removed outlier: 4.236A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR R 116 " --> pdb=" O HIS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 170 removed outlier: 3.783A pdb=" N ALA R 160 " --> pdb=" O ALA R 156 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU R 161 " --> pdb=" O VAL R 157 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA R 167 " --> pdb=" O TRP R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 176 removed outlier: 3.763A pdb=" N VAL R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE R 176 " --> pdb=" O PRO R 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 171 through 176' Processing helix chain 'R' and resid 200 through 217 removed outlier: 3.549A pdb=" N GLU R 204 " --> pdb=" O THR R 200 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE R 205 " --> pdb=" O ILE R 201 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP R 208 " --> pdb=" O GLU R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 244 removed outlier: 3.545A pdb=" N ARG R 240 " --> pdb=" O ALA R 236 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU R 241 " --> pdb=" O SER R 237 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL R 243 " --> pdb=" O LYS R 239 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 264 removed outlier: 3.588A pdb=" N VAL R 255 " --> pdb=" O HIS R 251 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER R 256 " --> pdb=" O GLN R 252 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN R 257 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE R 260 " --> pdb=" O SER R 256 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N AARG R 261 " --> pdb=" O GLN R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 294 removed outlier: 3.662A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER R 278 " --> pdb=" O PHE R 274 " (cutoff:3.500A) Proline residue: R 279 - end of helix removed outlier: 3.945A pdb=" N ASN R 291 " --> pdb=" O ILE R 287 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE R 292 " --> pdb=" O LEU R 288 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN R 294 " --> pdb=" O GLN R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 321 removed outlier: 3.567A pdb=" N ALA R 312 " --> pdb=" O ALA R 308 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.548A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.564A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.864A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.087A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.515A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 231 removed outlier: 6.557A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.590A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.758A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 141 through 143 removed outlier: 3.694A pdb=" N ALA S 212 " --> pdb=" O SER S 209 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 147 through 148 removed outlier: 6.633A pdb=" N LEU S 175 " --> pdb=" O TYR S 191 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR S 191 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TRP S 177 " --> pdb=" O LEU S 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.561A pdb=" N ASP A 200 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1111 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: 2.33 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2808 1.34 - 1.46: 1586 1.46 - 1.57: 4438 1.57 - 1.69: 1 1.69 - 1.81: 84 Bond restraints: 8917 Sorted by residual: bond pdb=" C LEU A 353 " pdb=" N PHE A 354 " ideal model delta sigma weight residual 1.329 1.296 0.033 1.40e-02 5.10e+03 5.65e+00 bond pdb=" N ARG R 71 " pdb=" CA ARG R 71 " ideal model delta sigma weight residual 1.458 1.485 -0.028 1.17e-02 7.31e+03 5.54e+00 bond pdb=" N ARG R 70 " pdb=" CA ARG R 70 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.44e+00 bond pdb=" N ARG R 69 " pdb=" CA ARG R 69 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.10e+00 bond pdb=" N ARG R 68 " pdb=" CA ARG R 68 " ideal model delta sigma weight residual 1.464 1.489 -0.025 1.30e-02 5.92e+03 3.78e+00 ... (remaining 8912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.40: 12068 5.40 - 10.80: 31 10.80 - 16.20: 1 16.20 - 21.59: 0 21.59 - 26.99: 2 Bond angle restraints: 12102 Sorted by residual: angle pdb=" CD ARG R 254 " pdb=" NE ARG R 254 " pdb=" CZ ARG R 254 " ideal model delta sigma weight residual 124.40 97.41 26.99 1.40e+00 5.10e-01 3.72e+02 angle pdb=" CA ASP R 259 " pdb=" CB ASP R 259 " pdb=" CG ASP R 259 " ideal model delta sigma weight residual 112.60 103.66 8.94 1.00e+00 1.00e+00 7.99e+01 angle pdb=" CA GLN R 258 " pdb=" CB GLN R 258 " pdb=" CG GLN R 258 " ideal model delta sigma weight residual 114.10 130.28 -16.18 2.00e+00 2.50e-01 6.55e+01 angle pdb=" CA LEU R 86 " pdb=" CB LEU R 86 " pdb=" CG LEU R 86 " ideal model delta sigma weight residual 116.30 141.78 -25.48 3.50e+00 8.16e-02 5.30e+01 angle pdb=" N VAL R 109 " pdb=" CA VAL R 109 " pdb=" C VAL R 109 " ideal model delta sigma weight residual 113.71 107.13 6.58 9.50e-01 1.11e+00 4.80e+01 ... (remaining 12097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4811 17.63 - 35.25: 374 35.25 - 52.88: 63 52.88 - 70.50: 18 70.50 - 88.13: 7 Dihedral angle restraints: 5273 sinusoidal: 1963 harmonic: 3310 Sorted by residual: dihedral pdb=" CD ARG R 69 " pdb=" NE ARG R 69 " pdb=" CZ ARG R 69 " pdb=" NH1 ARG R 69 " ideal model delta sinusoidal sigma weight residual 0.00 75.86 -75.86 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CB CYS S 160 " pdb=" SG CYS S 160 " pdb=" SG CYS S 230 " pdb=" CB CYS S 230 " ideal model delta sinusoidal sigma weight residual 93.00 158.16 -65.16 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CA HIS R 142 " pdb=" C HIS R 142 " pdb=" N LEU R 143 " pdb=" CA LEU R 143 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1223 0.066 - 0.132: 178 0.132 - 0.197: 11 0.197 - 0.263: 0 0.263 - 0.329: 2 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CB ILE R 89 " pdb=" CA ILE R 89 " pdb=" CG1 ILE R 89 " pdb=" CG2 ILE R 89 " both_signs ideal model delta sigma weight residual False 2.64 2.97 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C04 7NR R 401 " pdb=" C05 7NR R 401 " pdb=" C06 7NR R 401 " pdb=" O01 7NR R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.76 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA ARG R 71 " pdb=" N ARG R 71 " pdb=" C ARG R 71 " pdb=" CB ARG R 71 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.53e-01 ... (remaining 1411 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 69 " 1.062 9.50e-02 1.11e+02 4.76e-01 1.37e+02 pdb=" NE ARG R 69 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG R 69 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG R 69 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG R 69 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 115 " 0.082 2.00e-02 2.50e+03 5.02e-02 4.41e+01 pdb=" CG PHE R 115 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 PHE R 115 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 PHE R 115 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE R 115 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE R 115 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE R 115 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 68 " -0.569 9.50e-02 1.11e+02 2.55e-01 3.98e+01 pdb=" NE ARG R 68 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG R 68 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG R 68 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG R 68 " -0.018 2.00e-02 2.50e+03 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 764 2.74 - 3.28: 8404 3.28 - 3.82: 13890 3.82 - 4.36: 16479 4.36 - 4.90: 29602 Nonbonded interactions: 69139 Sorted by model distance: nonbonded pdb=" CD ARG R 254 " pdb=" NH1 ARG R 254 " model vdw 2.199 2.816 nonbonded pdb=" O ASN A 347 " pdb=" OD1 ASP A 350 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP B 228 " pdb=" NZ LYS A 209 " model vdw 2.277 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP Y 48 " model vdw 2.278 3.040 nonbonded pdb=" OE1 GLN A 52 " pdb=" ND2 ASN A 331 " model vdw 2.300 3.120 ... (remaining 69134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.820 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 8917 Z= 0.297 Angle : 0.854 26.993 12102 Z= 0.505 Chirality : 0.048 0.329 1414 Planarity : 0.015 0.476 1520 Dihedral : 13.646 88.129 3128 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.76 % Allowed : 0.33 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.24), residues: 1126 helix: -0.23 (0.27), residues: 372 sheet: -0.72 (0.30), residues: 289 loop : -1.57 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 104 HIS 0.004 0.001 HIS B 91 PHE 0.082 0.003 PHE R 115 TYR 0.013 0.001 TYR R 165 ARG 0.008 0.000 ARG S 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 1.141 Fit side-chains REVERT: B 290 ASP cc_start: 0.7274 (m-30) cc_final: 0.6962 (m-30) REVERT: A 229 ASP cc_start: 0.8172 (t70) cc_final: 0.7757 (t70) REVERT: A 245 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7288 (tm-30) REVERT: A 298 GLU cc_start: 0.7887 (pt0) cc_final: 0.7473 (pt0) REVERT: A 354 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.7052 (t80) outliers start: 6 outliers final: 1 residues processed: 161 average time/residue: 0.2346 time to fit residues: 50.8288 Evaluate side-chains 141 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 106 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 50.0000 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8917 Z= 0.241 Angle : 0.583 7.303 12102 Z= 0.309 Chirality : 0.043 0.155 1414 Planarity : 0.004 0.051 1520 Dihedral : 5.550 56.879 1250 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.87 % Allowed : 7.16 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1126 helix: 0.67 (0.28), residues: 365 sheet: -0.50 (0.30), residues: 297 loop : -1.29 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 207 HIS 0.005 0.001 HIS B 91 PHE 0.018 0.002 PHE R 177 TYR 0.016 0.001 TYR R 165 ARG 0.004 0.000 ARG R 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 1.045 Fit side-chains REVERT: B 290 ASP cc_start: 0.7290 (m-30) cc_final: 0.7077 (m-30) REVERT: S 203 ARG cc_start: 0.6115 (mtm110) cc_final: 0.5824 (mtm-85) REVERT: A 229 ASP cc_start: 0.7982 (t70) cc_final: 0.7443 (t70) REVERT: A 330 LYS cc_start: 0.8001 (mptt) cc_final: 0.7693 (mmtm) REVERT: A 354 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.6709 (t80) REVERT: R 178 ARG cc_start: 0.7080 (mmt90) cc_final: 0.6767 (mmm160) outliers start: 7 outliers final: 2 residues processed: 147 average time/residue: 0.2364 time to fit residues: 46.9189 Evaluate side-chains 140 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 109 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN A 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8917 Z= 0.158 Angle : 0.532 8.584 12102 Z= 0.278 Chirality : 0.041 0.144 1414 Planarity : 0.004 0.047 1520 Dihedral : 4.908 56.911 1248 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.30 % Allowed : 9.54 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 1126 helix: 0.93 (0.28), residues: 377 sheet: -0.33 (0.30), residues: 298 loop : -1.28 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 207 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE R 177 TYR 0.018 0.001 TYR R 165 ARG 0.003 0.000 ARG R 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.978 Fit side-chains REVERT: A 229 ASP cc_start: 0.7951 (t70) cc_final: 0.7392 (t70) REVERT: A 276 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: A 330 LYS cc_start: 0.7956 (mptt) cc_final: 0.7652 (mmtm) outliers start: 11 outliers final: 9 residues processed: 140 average time/residue: 0.2128 time to fit residues: 41.5278 Evaluate side-chains 135 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN A 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8917 Z= 0.152 Angle : 0.511 7.435 12102 Z= 0.268 Chirality : 0.041 0.142 1414 Planarity : 0.003 0.047 1520 Dihedral : 4.707 56.940 1248 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.95 % Allowed : 10.20 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1126 helix: 1.16 (0.29), residues: 378 sheet: -0.34 (0.29), residues: 298 loop : -1.17 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 207 HIS 0.003 0.001 HIS S 35 PHE 0.020 0.001 PHE S 68 TYR 0.012 0.001 TYR R 165 ARG 0.003 0.000 ARG R 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.975 Fit side-chains REVERT: B 259 GLN cc_start: 0.7433 (tt0) cc_final: 0.6568 (mt0) REVERT: A 229 ASP cc_start: 0.7889 (t70) cc_final: 0.7307 (t70) REVERT: A 240 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7321 (pmm) REVERT: A 274 PHE cc_start: 0.7319 (t80) cc_final: 0.7118 (t80) REVERT: A 276 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: A 330 LYS cc_start: 0.7941 (mptt) cc_final: 0.7650 (mmtm) outliers start: 17 outliers final: 12 residues processed: 136 average time/residue: 0.2286 time to fit residues: 43.6637 Evaluate side-chains 136 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 0.0170 chunk 44 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8917 Z= 0.307 Angle : 0.580 7.489 12102 Z= 0.307 Chirality : 0.044 0.150 1414 Planarity : 0.004 0.050 1520 Dihedral : 4.928 58.257 1248 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.49 % Allowed : 11.39 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1126 helix: 1.07 (0.28), residues: 380 sheet: -0.30 (0.30), residues: 304 loop : -1.31 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 36 HIS 0.006 0.001 HIS B 91 PHE 0.017 0.002 PHE S 68 TYR 0.014 0.002 TYR B 59 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.117 Fit side-chains REVERT: A 229 ASP cc_start: 0.7868 (t70) cc_final: 0.7255 (t70) REVERT: A 240 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7417 (pmm) REVERT: A 245 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7320 (tm-30) REVERT: A 276 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: A 330 LYS cc_start: 0.8026 (mptt) cc_final: 0.7721 (mmtm) outliers start: 22 outliers final: 18 residues processed: 139 average time/residue: 0.2327 time to fit residues: 43.7438 Evaluate side-chains 144 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8917 Z= 0.188 Angle : 0.536 9.755 12102 Z= 0.280 Chirality : 0.042 0.139 1414 Planarity : 0.004 0.049 1520 Dihedral : 4.846 57.397 1248 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.17 % Allowed : 12.26 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1126 helix: 1.23 (0.29), residues: 380 sheet: -0.19 (0.30), residues: 303 loop : -1.26 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 104 HIS 0.004 0.001 HIS B 91 PHE 0.014 0.001 PHE S 68 TYR 0.010 0.001 TYR B 59 ARG 0.007 0.000 ARG R 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7891 (t70) cc_final: 0.7293 (t70) REVERT: A 245 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7249 (tm-30) REVERT: A 276 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: A 330 LYS cc_start: 0.7979 (mptt) cc_final: 0.7683 (mmtm) REVERT: R 104 TRP cc_start: 0.8420 (t-100) cc_final: 0.8214 (t60) outliers start: 19 outliers final: 17 residues processed: 130 average time/residue: 0.2204 time to fit residues: 39.7314 Evaluate side-chains 140 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8917 Z= 0.215 Angle : 0.541 8.739 12102 Z= 0.283 Chirality : 0.042 0.142 1414 Planarity : 0.004 0.050 1520 Dihedral : 4.725 57.304 1248 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.28 % Allowed : 12.69 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1126 helix: 1.30 (0.29), residues: 380 sheet: -0.16 (0.30), residues: 303 loop : -1.23 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 207 HIS 0.004 0.001 HIS B 91 PHE 0.021 0.001 PHE S 68 TYR 0.011 0.001 TYR B 59 ARG 0.006 0.000 ARG R 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.953 Fit side-chains REVERT: A 229 ASP cc_start: 0.7930 (t70) cc_final: 0.7302 (t70) REVERT: A 240 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6992 (pmm) REVERT: A 245 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7239 (tm-30) REVERT: A 276 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: R 104 TRP cc_start: 0.8474 (t-100) cc_final: 0.8240 (t60) outliers start: 20 outliers final: 17 residues processed: 134 average time/residue: 0.2267 time to fit residues: 41.3251 Evaluate side-chains 142 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 242 THR Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 0.0770 chunk 97 optimal weight: 0.0020 chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 overall best weight: 0.5748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN A 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8917 Z= 0.141 Angle : 0.502 7.916 12102 Z= 0.261 Chirality : 0.041 0.138 1414 Planarity : 0.003 0.048 1520 Dihedral : 4.481 56.296 1248 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.74 % Allowed : 13.56 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 1126 helix: 1.47 (0.29), residues: 379 sheet: -0.03 (0.30), residues: 288 loop : -1.15 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 207 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.001 PHE S 68 TYR 0.008 0.001 TYR R 165 ARG 0.006 0.000 ARG R 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.154 Fit side-chains REVERT: A 229 ASP cc_start: 0.7900 (t70) cc_final: 0.7259 (t70) REVERT: A 240 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6937 (pmm) REVERT: A 276 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: A 330 LYS cc_start: 0.7955 (mptt) cc_final: 0.7648 (mmtm) outliers start: 15 outliers final: 13 residues processed: 136 average time/residue: 0.2295 time to fit residues: 42.6745 Evaluate side-chains 138 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.0980 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8917 Z= 0.208 Angle : 0.553 14.731 12102 Z= 0.282 Chirality : 0.042 0.175 1414 Planarity : 0.003 0.050 1520 Dihedral : 4.539 56.676 1248 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.95 % Allowed : 14.21 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1126 helix: 1.41 (0.29), residues: 382 sheet: -0.07 (0.30), residues: 296 loop : -1.12 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 104 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.001 PHE S 68 TYR 0.009 0.001 TYR R 165 ARG 0.006 0.000 ARG R 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.021 Fit side-chains REVERT: A 229 ASP cc_start: 0.7877 (t70) cc_final: 0.7226 (t70) REVERT: A 240 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6967 (pmm) REVERT: A 245 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7239 (tm-30) REVERT: A 276 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: A 330 LYS cc_start: 0.7952 (mptt) cc_final: 0.7668 (mmtm) REVERT: R 104 TRP cc_start: 0.8109 (t60) cc_final: 0.7802 (t60) outliers start: 17 outliers final: 13 residues processed: 132 average time/residue: 0.2248 time to fit residues: 40.6155 Evaluate side-chains 140 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 242 THR Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8917 Z= 0.152 Angle : 0.524 13.433 12102 Z= 0.267 Chirality : 0.041 0.138 1414 Planarity : 0.003 0.050 1520 Dihedral : 4.396 55.899 1248 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.63 % Allowed : 14.75 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1126 helix: 1.49 (0.29), residues: 382 sheet: 0.03 (0.30), residues: 292 loop : -1.00 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 104 HIS 0.003 0.001 HIS S 35 PHE 0.015 0.001 PHE S 68 TYR 0.008 0.001 TYR R 165 ARG 0.006 0.000 ARG R 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.973 Fit side-chains REVERT: S 93 MET cc_start: 0.7345 (ttt) cc_final: 0.7130 (ttt) REVERT: A 229 ASP cc_start: 0.7881 (t70) cc_final: 0.7234 (t70) REVERT: A 240 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6895 (pmm) REVERT: A 276 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: A 330 LYS cc_start: 0.7956 (mptt) cc_final: 0.7668 (mmtm) outliers start: 14 outliers final: 12 residues processed: 128 average time/residue: 0.2271 time to fit residues: 39.9421 Evaluate side-chains 134 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.161278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112859 restraints weight = 26701.451| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.90 r_work: 0.3103 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8917 Z= 0.184 Angle : 0.537 13.052 12102 Z= 0.276 Chirality : 0.042 0.140 1414 Planarity : 0.003 0.051 1520 Dihedral : 4.427 55.972 1248 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.74 % Allowed : 15.29 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1126 helix: 1.55 (0.29), residues: 377 sheet: -0.00 (0.30), residues: 293 loop : -1.01 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 104 HIS 0.004 0.001 HIS B 91 PHE 0.015 0.001 PHE S 68 TYR 0.009 0.001 TYR A 302 ARG 0.006 0.000 ARG R 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2124.38 seconds wall clock time: 39 minutes 26.39 seconds (2366.39 seconds total)