Starting phenix.real_space_refine on Sat Aug 3 02:31:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/08_2024/8uo3_42426.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/08_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_42426/08_2024/8uo3_42426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/08_2024/8uo3_42426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/08_2024/8uo3_42426.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/08_2024/8uo3_42426.cif" } 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 4.98, per 1000 atoms: 0.75 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: 2.81 Conformation dependent library (CDL) restraints added in 1.4 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... Secondary structure from input PDB file: 33 helices and 8 sheets defined 49.2% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 4.187A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) 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 52 through 65 removed outlier: 3.797A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) 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 90 through 109 removed outlier: 4.141A pdb=" N ASP A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) 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 113 Processing helix chain 'A' and resid 124 through 135 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 156 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 156 through 165 removed outlier: 4.049A pdb=" N ARG A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 removed outlier: 3.504A pdb=" N PHE A 178 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 187 removed outlier: 3.888A pdb=" N GLN A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 199 removed outlier: 3.656A pdb=" N ARG A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 removed outlier: 4.033A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.772A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.016A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 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) Processing helix chain 'A' and resid 331 through 352 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) removed outlier: 4.196A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.798A pdb=" N ILE A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) 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) removed outlier: 3.692A pdb=" N ILE A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.623A pdb=" N HIS A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 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) removed outlier: 3.562A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.619A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.690A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'G' and resid 8 through 24 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) removed outlier: 3.693A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 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) removed outlier: 3.535A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 46 Processing helix chain 'R' and resid 46 through 58 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 66 through 95 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 104 through 137 removed outlier: 3.973A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) 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 172 Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 198 through 208 removed outlier: 3.645A pdb=" N ALA R 202 " --> pdb=" O ALA R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 232 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 294 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 Processing helix chain 'R' and resid 306 through 327 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=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.543A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.789A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, 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=AA4, 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) removed outlier: 6.979A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.761A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.797A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AA7, 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=AA8, first strand: chain 'B' and resid 276 through 277 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) 316 hydrogen bonds defined for protein. 918 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: 1.90 Time building geometry restraints manager: 3.08 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: 1392 2.78 - 3.31: 6289 3.31 - 3.84: 9933 3.84 - 4.37: 10595 4.37 - 4.90: 19112 Nonbonded interactions: 47321 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.246 3.040 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 3.040 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 3.120 ... (remaining 47316 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=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: 2.360 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 23.410 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.920 ------------------------------------------------------------------------------- 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= 0.409 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 : 0.731 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.1877 time to fit residues: 20.8432 Evaluate side-chains 66 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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: 0.9990 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 chunk 38 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- 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** B 311 HIS R 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6770 Z= 0.243 Angle : 0.534 7.202 9272 Z= 0.290 Chirality : 0.043 0.154 1111 Planarity : 0.003 0.032 1198 Dihedral : 10.219 163.327 1054 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.79 % Allowed : 9.86 % Favored : 89.35 % 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: 0.06 (0.27), residues: 949 helix: 1.81 (0.26), residues: 399 sheet: -1.33 (0.38), residues: 171 loop : -1.21 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 313 HIS 0.005 0.001 HIS B 183 PHE 0.014 0.001 PHE B 241 TYR 0.013 0.001 TYR R 326 ARG 0.003 0.000 ARG B 251 *********************** 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: 4 poor density : 66 time to evaluate : 0.762 Fit side-chains REVERT: B 292 PHE cc_start: 0.8520 (m-80) cc_final: 0.8276 (m-10) REVERT: R 194 PHE cc_start: 0.7755 (m-80) cc_final: 0.7296 (m-80) outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.1403 time to fit residues: 14.2351 Evaluate side-chains 66 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR 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: 0.4980 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6770 Z= 0.209 Angle : 0.489 5.989 9272 Z= 0.266 Chirality : 0.042 0.146 1111 Planarity : 0.003 0.030 1198 Dihedral : 8.749 151.712 1054 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.79 % Allowed : 12.62 % Favored : 86.59 % 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: 2.10 (0.26), residues: 403 sheet: -1.14 (0.38), residues: 168 loop : -1.25 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 313 HIS 0.005 0.001 HIS B 183 PHE 0.012 0.001 PHE B 241 TYR 0.016 0.001 TYR R 219 ARG 0.002 0.000 ARG B 219 *********************** 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 74 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.738 Fit side-chains REVERT: B 95 LEU cc_start: 0.9159 (mt) cc_final: 0.8936 (mt) REVERT: B 292 PHE cc_start: 0.8786 (m-80) cc_final: 0.8403 (m-10) outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.1501 time to fit residues: 15.7973 Evaluate side-chains 64 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 173 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 9 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 0.0370 chunk 24 optimal weight: 3.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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: 0.8128 moved from start: 0.2013 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= 0.116 Angle : 0.436 5.641 9272 Z= 0.234 Chirality : 0.040 0.141 1111 Planarity : 0.003 0.028 1198 Dihedral : 7.634 140.165 1054 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.37 % Allowed : 12.23 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.28), residues: 949 helix: 2.26 (0.26), residues: 411 sheet: -0.92 (0.38), residues: 168 loop : -1.14 (0.30), residues: 370 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 0.013 0.001 PHE R 194 TYR 0.012 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 79 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.812 Fit side-chains REVERT: B 292 PHE cc_start: 0.8769 (m-10) cc_final: 0.8437 (m-10) REVERT: R 194 PHE cc_start: 0.7505 (m-80) cc_final: 0.7026 (m-80) outliers start: 12 outliers final: 5 residues processed: 76 average time/residue: 0.1420 time to fit residues: 16.0325 Evaluate side-chains 69 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 284 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 6770 Z= 0.445 Angle : 0.593 5.849 9272 Z= 0.324 Chirality : 0.045 0.163 1111 Planarity : 0.004 0.032 1198 Dihedral : 8.141 141.260 1054 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.56 % Allowed : 13.81 % Favored : 83.63 % 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: -0.01 (0.27), residues: 949 helix: 1.79 (0.26), residues: 413 sheet: -1.27 (0.38), residues: 168 loop : -1.47 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 63 HIS 0.008 0.002 HIS B 183 PHE 0.024 0.002 PHE B 241 TYR 0.014 0.002 TYR A 360 ARG 0.003 0.001 ARG B 219 *********************** 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 78 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.838 Fit side-chains REVERT: B 142 HIS cc_start: 0.9136 (OUTLIER) cc_final: 0.8935 (t-170) REVERT: B 292 PHE cc_start: 0.9035 (m-10) cc_final: 0.8595 (m-10) REVERT: R 194 PHE cc_start: 0.7486 (m-80) cc_final: 0.6787 (m-80) outliers start: 13 outliers final: 7 residues processed: 74 average time/residue: 0.1336 time to fit residues: 14.8082 Evaluate side-chains 68 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 334 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2171 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= 0.164 Angle : 0.470 7.428 9272 Z= 0.253 Chirality : 0.041 0.149 1111 Planarity : 0.003 0.060 1198 Dihedral : 7.544 135.236 1054 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.58 % Allowed : 15.98 % Favored : 82.45 % 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: 0.25 (0.28), residues: 949 helix: 2.02 (0.26), residues: 416 sheet: -1.09 (0.38), residues: 168 loop : -1.42 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 313 HIS 0.003 0.001 HIS A 357 PHE 0.011 0.001 PHE R 289 TYR 0.010 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 76 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.743 Fit side-chains REVERT: B 292 PHE cc_start: 0.8980 (m-10) cc_final: 0.8552 (m-10) REVERT: R 194 PHE cc_start: 0.7461 (m-80) cc_final: 0.6750 (m-80) outliers start: 8 outliers final: 6 residues processed: 73 average time/residue: 0.1402 time to fit residues: 15.1774 Evaluate side-chains 71 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6770 Z= 0.186 Angle : 0.480 6.280 9272 Z= 0.259 Chirality : 0.041 0.146 1111 Planarity : 0.003 0.045 1198 Dihedral : 7.229 130.909 1054 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.78 % Allowed : 17.36 % Favored : 80.87 % 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: 0.42 (0.28), residues: 949 helix: 2.09 (0.26), residues: 418 sheet: -0.94 (0.39), residues: 163 loop : -1.30 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.007 0.001 HIS B 142 PHE 0.012 0.001 PHE A 222 TYR 0.010 0.001 TYR R 219 ARG 0.002 0.000 ARG A 380 *********************** 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: 9 poor density : 68 time to evaluate : 0.808 Fit side-chains REVERT: B 292 PHE cc_start: 0.8978 (m-10) cc_final: 0.8520 (m-10) REVERT: R 194 PHE cc_start: 0.7469 (m-80) cc_final: 0.6709 (m-80) outliers start: 9 outliers final: 7 residues processed: 73 average time/residue: 0.1482 time to fit residues: 16.1735 Evaluate side-chains 73 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 257 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8182 moved from start: 0.2356 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= 0.158 Angle : 0.460 5.923 9272 Z= 0.246 Chirality : 0.041 0.142 1111 Planarity : 0.003 0.035 1198 Dihedral : 6.849 125.613 1054 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.97 % Allowed : 17.75 % 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: 0.47 (0.28), residues: 949 helix: 2.08 (0.26), residues: 426 sheet: -0.88 (0.39), residues: 163 loop : -1.30 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 313 HIS 0.007 0.001 HIS B 142 PHE 0.010 0.001 PHE B 241 TYR 0.009 0.001 TYR R 219 ARG 0.001 0.000 ARG B 219 *********************** 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 77 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.837 Fit side-chains REVERT: B 292 PHE cc_start: 0.8961 (m-10) cc_final: 0.8516 (m-10) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.1473 time to fit residues: 16.1765 Evaluate side-chains 73 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 257 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 45 MET 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: 5.9990 chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6770 Z= 0.389 Angle : 0.564 6.352 9272 Z= 0.305 Chirality : 0.044 0.156 1111 Planarity : 0.003 0.031 1198 Dihedral : 7.373 129.779 1054 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.97 % Allowed : 17.55 % 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: 0.03 (0.27), residues: 949 helix: 1.79 (0.26), residues: 422 sheet: -1.15 (0.39), residues: 167 loop : -1.55 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.007 0.001 HIS B 142 PHE 0.018 0.002 PHE B 241 TYR 0.012 0.001 TYR A 358 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 70 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.700 Fit side-chains REVERT: B 142 HIS cc_start: 0.9199 (OUTLIER) cc_final: 0.8870 (t70) REVERT: B 292 PHE cc_start: 0.9053 (m-10) cc_final: 0.8614 (m-10) outliers start: 10 outliers final: 5 residues processed: 67 average time/residue: 0.1402 time to fit residues: 14.0103 Evaluate side-chains 65 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 142 HIS 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: 0.8980 chunk 62 optimal weight: 0.0570 chunk 94 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 7 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6770 Z= 0.149 Angle : 0.469 6.760 9272 Z= 0.251 Chirality : 0.041 0.142 1111 Planarity : 0.003 0.030 1198 Dihedral : 6.728 121.522 1054 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.58 % Allowed : 18.15 % 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: 0.32 (0.28), residues: 949 helix: 2.00 (0.27), residues: 422 sheet: -0.94 (0.40), residues: 160 loop : -1.40 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 332 HIS 0.006 0.001 HIS B 142 PHE 0.009 0.001 PHE R 289 TYR 0.009 0.001 TYR R 219 ARG 0.001 0.000 ARG A 20 ********************** 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 71 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.954 Fit side-chains REVERT: B 120 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8799 (mm) REVERT: B 142 HIS cc_start: 0.9001 (OUTLIER) cc_final: 0.8524 (t70) REVERT: B 292 PHE cc_start: 0.8989 (m-10) cc_final: 0.8565 (m-10) REVERT: B 301 LYS cc_start: 0.8881 (mmtm) cc_final: 0.8670 (mmtt) outliers start: 8 outliers final: 3 residues processed: 67 average time/residue: 0.1443 time to fit residues: 14.3000 Evaluate side-chains 67 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 HIS 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: 3.9990 chunk 11 optimal weight: 0.0170 chunk 20 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103978 restraints weight = 11941.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.106918 restraints weight = 6495.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108868 restraints weight = 4523.979| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6770 Z= 0.157 Angle : 0.465 6.578 9272 Z= 0.248 Chirality : 0.041 0.143 1111 Planarity : 0.003 0.030 1198 Dihedral : 6.467 117.026 1054 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: 0.44 (0.28), residues: 949 helix: 2.07 (0.27), residues: 423 sheet: -0.83 (0.40), residues: 162 loop : -1.35 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 313 HIS 0.006 0.001 HIS B 142 PHE 0.010 0.001 PHE B 199 TYR 0.010 0.001 TYR R 219 ARG 0.001 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1436.79 seconds wall clock time: 29 minutes 31.54 seconds (1771.54 seconds total)