Starting phenix.real_space_refine on Tue May 7 03:46:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/05_2024/8uo3_42426_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/05_2024/8uo3_42426.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/8uo3_42426/05_2024/8uo3_42426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/05_2024/8uo3_42426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/05_2024/8uo3_42426_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/05_2024/8uo3_42426_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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 4187 2.51 5 N 1204 2.21 5 O 1222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 6650 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2559 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 13, 'TRANS': 345} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 425 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 337 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 20, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 286 Chain: "B" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2418 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 8, 'ARG:plan': 10, 'ASN:plan1': 5, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 148 Chain: "G" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 352 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1273 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 540 Unresolved non-hydrogen angles: 714 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 11, 'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 255 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.25, per 1000 atoms: 0.64 Number of scatterers: 6650 At special positions: 0 Unit cell: (82.4315, 134.493, 102.389, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 3 15.00 Mg 1 11.99 O 1222 8.00 N 1204 7.00 C 4187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.5 seconds 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1858 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 8 sheets defined 44.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 4.097A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.708A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 108 removed outlier: 3.704A pdb=" N ILE A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 96 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 125 through 134 removed outlier: 3.897A pdb=" N ASP A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.587A pdb=" N GLU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 153 " --> pdb=" O HIS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.550A pdb=" N LYS A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ASP A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 233 through 237 removed outlier: 4.033A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 removed outlier: 3.772A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.715A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 317' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.758A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.815A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.775A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (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 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'G' and resid 8 through 23 removed outlier: 4.003A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 removed outlier: 4.438A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 57 removed outlier: 3.990A pdb=" N ILE R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 94 removed outlier: 4.028A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA R 76 " --> pdb=" O ILE R 72 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL R 81 " --> pdb=" O CYS R 77 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY R 83 " --> pdb=" O ASP R 79 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU R 84 " --> pdb=" O LEU R 80 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 105 through 136 removed outlier: 3.513A pdb=" N TRP R 109 " --> pdb=" O TRP R 105 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR R 110 " --> pdb=" O CYS R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 171 Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 179 through 185 Processing helix chain 'R' and resid 199 through 207 Processing helix chain 'R' and resid 209 through 231 removed outlier: 3.533A pdb=" N PHE R 217 " --> pdb=" O VAL R 213 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 295 removed outlier: 4.336A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.615A pdb=" N VAL R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 326 removed outlier: 4.921A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 3.894A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.082A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 113 removed outlier: 3.523A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.768A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.528A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.769A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.751A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.606A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 846 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: 1.80 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1376 1.33 - 1.45: 1590 1.45 - 1.57: 3754 1.57 - 1.69: 5 1.69 - 1.81: 45 Bond restraints: 6770 Sorted by residual: bond pdb=" C VAL A 375 " pdb=" O VAL A 375 " ideal model delta sigma weight residual 1.237 1.290 -0.053 1.17e-02 7.31e+03 2.04e+01 bond pdb=" C ARG A 374 " pdb=" O ARG A 374 " ideal model delta sigma weight residual 1.235 1.290 -0.055 1.40e-02 5.10e+03 1.57e+01 bond pdb=" N VAL R 222 " pdb=" CA VAL R 222 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N VAL R 216 " pdb=" CA VAL R 216 " ideal model delta sigma weight residual 1.461 1.499 -0.039 1.19e-02 7.06e+03 1.06e+01 bond pdb=" N ARG A 374 " pdb=" CA ARG A 374 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.28e-02 6.10e+03 9.90e+00 ... (remaining 6765 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.31: 153 106.31 - 113.30: 3726 113.30 - 120.28: 2423 120.28 - 127.27: 2898 127.27 - 134.26: 72 Bond angle restraints: 9272 Sorted by residual: angle pdb=" N TYR R 199 " pdb=" CA TYR R 199 " pdb=" C TYR R 199 " ideal model delta sigma weight residual 111.28 103.70 7.58 1.09e+00 8.42e-01 4.84e+01 angle pdb=" N GLN A 384 " pdb=" CA GLN A 384 " pdb=" C GLN A 384 " ideal model delta sigma weight residual 111.71 105.11 6.60 1.15e+00 7.56e-01 3.30e+01 angle pdb=" N ASN R 196 " pdb=" CA ASN R 196 " pdb=" C ASN R 196 " ideal model delta sigma weight residual 109.65 101.00 8.65 1.56e+00 4.11e-01 3.07e+01 angle pdb=" C THR R 164 " pdb=" N SER R 165 " pdb=" CA SER R 165 " ideal model delta sigma weight residual 122.54 113.57 8.97 1.65e+00 3.67e-01 2.96e+01 angle pdb=" C TYR R 209 " pdb=" N VAL R 210 " pdb=" CA VAL R 210 " ideal model delta sigma weight residual 120.24 116.93 3.31 6.30e-01 2.52e+00 2.76e+01 ... (remaining 9267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.24: 3890 35.24 - 70.48: 54 70.48 - 105.71: 4 105.71 - 140.95: 3 140.95 - 176.19: 2 Dihedral angle restraints: 3953 sinusoidal: 1106 harmonic: 2847 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -71.60 176.19 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 109.41 151.46 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual 303.79 174.17 129.62 1 2.00e+01 2.50e-03 3.93e+01 ... (remaining 3950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 851 0.056 - 0.111: 178 0.111 - 0.167: 56 0.167 - 0.223: 20 0.223 - 0.278: 6 Chirality restraints: 1111 Sorted by residual: chirality pdb=" CA ILE G 9 " pdb=" N ILE G 9 " pdb=" C ILE G 9 " pdb=" CB ILE G 9 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ILE A 382 " pdb=" N ILE A 382 " pdb=" C ILE A 382 " pdb=" CB ILE A 382 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C3' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C4' GTP A 401 " pdb=" O3' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1108 not shown) Planarity restraints: 1198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 373 " 0.023 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C ARG A 373 " -0.077 2.00e-02 2.50e+03 pdb=" O ARG A 373 " 0.028 2.00e-02 2.50e+03 pdb=" N ARG A 374 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 195 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C THR R 195 " 0.070 2.00e-02 2.50e+03 pdb=" O THR R 195 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN R 196 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 153 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C ILE R 153 " 0.064 2.00e-02 2.50e+03 pdb=" O ILE R 153 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE R 154 " -0.022 2.00e-02 2.50e+03 ... (remaining 1195 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1395 2.78 - 3.31: 6313 3.31 - 3.84: 9966 3.84 - 4.37: 10648 4.37 - 4.90: 19115 Nonbonded interactions: 47437 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.246 2.440 nonbonded pdb=" O ASN A 377 " pdb=" CG ARG A 380 " model vdw 2.259 3.440 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.271 2.440 nonbonded pdb=" O HIS R 172 " pdb=" C TRP R 173 " model vdw 2.273 3.270 nonbonded pdb=" OD1 ASP A 223 " pdb=" N VAL A 224 " model vdw 2.275 2.520 ... (remaining 47432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.670 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.730 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.006 0.055 6770 Z= 0.425 Angle : 0.871 10.363 9272 Z= 0.604 Chirality : 0.059 0.278 1111 Planarity : 0.005 0.119 1198 Dihedral : 14.929 176.189 2095 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.20 % Allowed : 0.39 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.27), residues: 949 helix: 2.09 (0.27), residues: 363 sheet: -1.17 (0.38), residues: 174 loop : -1.13 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 154 HIS 0.003 0.001 HIS B 183 PHE 0.024 0.001 PHE A 376 TYR 0.014 0.001 TYR R 326 ARG 0.002 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.787 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.1625 time to fit residues: 18.1951 Evaluate side-chains 66 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 38 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6770 Z= 0.190 Angle : 0.493 6.640 9272 Z= 0.266 Chirality : 0.042 0.154 1111 Planarity : 0.003 0.029 1198 Dihedral : 9.943 161.724 1054 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.59 % Allowed : 9.27 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.27), residues: 949 helix: 1.74 (0.26), residues: 396 sheet: -1.05 (0.39), residues: 168 loop : -1.13 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 313 HIS 0.004 0.001 HIS B 183 PHE 0.011 0.001 PHE B 241 TYR 0.012 0.001 TYR R 316 ARG 0.002 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.939 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 69 average time/residue: 0.1566 time to fit residues: 15.7486 Evaluate side-chains 63 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 173 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 0.0970 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6770 Z= 0.156 Angle : 0.442 5.537 9272 Z= 0.237 Chirality : 0.040 0.143 1111 Planarity : 0.003 0.029 1198 Dihedral : 8.498 151.081 1054 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.18 % Allowed : 11.24 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.27), residues: 949 helix: 2.02 (0.26), residues: 398 sheet: -1.14 (0.38), residues: 174 loop : -1.10 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 313 HIS 0.003 0.001 HIS B 183 PHE 0.010 0.001 PHE B 241 TYR 0.014 0.001 TYR R 219 ARG 0.001 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.795 Fit side-chains REVERT: B 95 LEU cc_start: 0.9110 (mt) cc_final: 0.8890 (mt) REVERT: R 194 PHE cc_start: 0.7743 (m-80) cc_final: 0.7226 (m-80) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.1437 time to fit residues: 14.4615 Evaluate side-chains 67 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain R residue 326 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.0030 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 9 optimal weight: 0.0570 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 0.0000 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 0.0050 chunk 24 optimal weight: 0.6980 overall best weight: 0.1526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.023 6770 Z= 0.101 Angle : 0.410 5.791 9272 Z= 0.217 Chirality : 0.039 0.142 1111 Planarity : 0.002 0.028 1198 Dihedral : 7.414 138.849 1054 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.18 % Allowed : 12.82 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.27), residues: 949 helix: 2.22 (0.26), residues: 408 sheet: -0.98 (0.39), residues: 164 loop : -1.10 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 313 HIS 0.002 0.000 HIS A 357 PHE 0.014 0.001 PHE R 139 TYR 0.011 0.001 TYR R 219 ARG 0.002 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.647 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 0.1384 time to fit residues: 14.3410 Evaluate side-chains 67 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain R residue 326 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 78 optimal weight: 0.0000 chunk 63 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6770 Z= 0.144 Angle : 0.422 5.669 9272 Z= 0.225 Chirality : 0.040 0.157 1111 Planarity : 0.002 0.027 1198 Dihedral : 7.118 134.788 1054 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.17 % Allowed : 14.00 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.28), residues: 949 helix: 2.38 (0.26), residues: 408 sheet: -0.75 (0.40), residues: 159 loop : -1.10 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 313 HIS 0.003 0.001 HIS B 183 PHE 0.010 0.001 PHE B 241 TYR 0.008 0.001 TYR R 219 ARG 0.002 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.759 Fit side-chains REVERT: B 292 PHE cc_start: 0.8597 (m-10) cc_final: 0.8286 (m-10) outliers start: 11 outliers final: 6 residues processed: 75 average time/residue: 0.1358 time to fit residues: 15.2023 Evaluate side-chains 72 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 326 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 0.0370 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 91 optimal weight: 0.0870 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 48 optimal weight: 0.0870 chunk 88 optimal weight: 1.9990 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6770 Z= 0.108 Angle : 0.413 7.161 9272 Z= 0.217 Chirality : 0.039 0.142 1111 Planarity : 0.002 0.026 1198 Dihedral : 6.705 128.403 1054 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.58 % Allowed : 14.99 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.28), residues: 949 helix: 2.45 (0.26), residues: 408 sheet: -0.70 (0.41), residues: 161 loop : -1.09 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 313 HIS 0.002 0.000 HIS B 142 PHE 0.015 0.001 PHE R 194 TYR 0.009 0.001 TYR R 219 ARG 0.001 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.708 Fit side-chains REVERT: B 292 PHE cc_start: 0.8645 (m-10) cc_final: 0.8346 (m-10) REVERT: R 194 PHE cc_start: 0.7563 (m-80) cc_final: 0.7194 (m-80) outliers start: 8 outliers final: 5 residues processed: 73 average time/residue: 0.1456 time to fit residues: 15.9390 Evaluate side-chains 70 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 326 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6770 Z= 0.321 Angle : 0.520 7.294 9272 Z= 0.279 Chirality : 0.043 0.154 1111 Planarity : 0.003 0.028 1198 Dihedral : 7.164 130.833 1054 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.17 % Allowed : 15.78 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 949 helix: 2.25 (0.27), residues: 402 sheet: -0.80 (0.39), residues: 169 loop : -1.19 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.007 0.001 HIS B 183 PHE 0.019 0.002 PHE B 241 TYR 0.012 0.001 TYR A 360 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.788 Fit side-chains REVERT: B 292 PHE cc_start: 0.8924 (m-10) cc_final: 0.8492 (m-10) REVERT: R 194 PHE cc_start: 0.7495 (m-80) cc_final: 0.6998 (m-80) outliers start: 11 outliers final: 10 residues processed: 74 average time/residue: 0.1382 time to fit residues: 15.2873 Evaluate side-chains 73 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 326 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.1980 chunk 27 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 0.0570 chunk 8 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 overall best weight: 0.4900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6770 Z= 0.132 Angle : 0.436 6.302 9272 Z= 0.231 Chirality : 0.040 0.142 1111 Planarity : 0.002 0.028 1198 Dihedral : 6.498 121.803 1054 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.17 % Allowed : 16.37 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.28), residues: 949 helix: 2.44 (0.27), residues: 407 sheet: -0.79 (0.39), residues: 170 loop : -1.19 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 154 HIS 0.003 0.001 HIS B 142 PHE 0.009 0.001 PHE R 139 TYR 0.009 0.001 TYR R 219 ARG 0.001 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.765 Fit side-chains REVERT: B 292 PHE cc_start: 0.8862 (m-10) cc_final: 0.8446 (m-10) REVERT: R 194 PHE cc_start: 0.7584 (m-80) cc_final: 0.7052 (m-80) outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 0.1367 time to fit residues: 14.2697 Evaluate side-chains 70 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6770 Z= 0.314 Angle : 0.509 6.538 9272 Z= 0.272 Chirality : 0.042 0.152 1111 Planarity : 0.003 0.029 1198 Dihedral : 6.827 123.882 1054 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.97 % Allowed : 16.96 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.28), residues: 949 helix: 2.19 (0.27), residues: 407 sheet: -0.86 (0.39), residues: 169 loop : -1.21 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.006 0.001 HIS B 183 PHE 0.016 0.002 PHE B 241 TYR 0.010 0.001 TYR B 111 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.804 Fit side-chains REVERT: B 142 HIS cc_start: 0.8951 (OUTLIER) cc_final: 0.8682 (t-170) REVERT: B 292 PHE cc_start: 0.8952 (m-10) cc_final: 0.8557 (m-10) REVERT: R 194 PHE cc_start: 0.7548 (m-80) cc_final: 0.6966 (m-80) outliers start: 10 outliers final: 7 residues processed: 70 average time/residue: 0.1390 time to fit residues: 14.6286 Evaluate side-chains 71 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 94 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 23 optimal weight: 0.1980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6770 Z= 0.143 Angle : 0.441 6.267 9272 Z= 0.234 Chirality : 0.040 0.145 1111 Planarity : 0.003 0.028 1198 Dihedral : 6.358 117.546 1054 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.58 % Allowed : 17.95 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.28), residues: 949 helix: 2.38 (0.27), residues: 402 sheet: -0.75 (0.39), residues: 169 loop : -1.19 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 154 HIS 0.003 0.001 HIS B 142 PHE 0.009 0.001 PHE B 241 TYR 0.008 0.001 TYR R 219 ARG 0.001 0.000 ARG A 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.777 Fit side-chains REVERT: B 292 PHE cc_start: 0.8923 (m-10) cc_final: 0.8478 (m-10) REVERT: R 194 PHE cc_start: 0.7491 (m-80) cc_final: 0.6899 (m-80) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.1373 time to fit residues: 14.3525 Evaluate side-chains 72 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 4.9990 chunk 11 optimal weight: 0.0270 chunk 20 optimal weight: 0.1980 chunk 75 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.136949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106286 restraints weight = 11908.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109312 restraints weight = 6505.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.111283 restraints weight = 4539.106| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6770 Z= 0.142 Angle : 0.433 5.976 9272 Z= 0.228 Chirality : 0.040 0.140 1111 Planarity : 0.002 0.028 1198 Dihedral : 6.022 111.263 1054 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.78 % Allowed : 17.95 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.28), residues: 949 helix: 2.51 (0.27), residues: 402 sheet: -0.71 (0.41), residues: 159 loop : -1.20 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 154 HIS 0.003 0.001 HIS B 142 PHE 0.009 0.001 PHE B 241 TYR 0.009 0.001 TYR R 219 ARG 0.001 0.000 ARG A 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1476.15 seconds wall clock time: 27 minutes 38.07 seconds (1658.07 seconds total)