Starting phenix.real_space_refine on Wed Sep 25 18:09:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/09_2024/6x1a_21994.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/09_2024/6x1a_21994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/09_2024/6x1a_21994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/09_2024/6x1a_21994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/09_2024/6x1a_21994.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/09_2024/6x1a_21994.cif" } resolution = 2.5 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 849 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 59 5.16 5 C 6444 2.51 5 N 1746 2.21 5 O 1890 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10140 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2873 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 337} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3206 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 64 Unusual residues: {'UK4': 1} Classifications: {'undetermined': 1, 'water': 23} Link IDs: {None: 23} Time building chain proxies: 5.98, per 1000 atoms: 0.59 Number of scatterers: 10140 At special positions: 0 Unit cell: (112.05, 99.6, 164.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 F 1 9.00 O 1890 8.00 N 1746 7.00 C 6444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 43.2% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 4.071A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 90 through 113 removed outlier: 4.130A pdb=" N ASP A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 143 through 154 removed outlier: 4.359A pdb=" N TYR A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.541A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.752A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.622A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.892A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.875A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 16 removed outlier: 3.633A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.658A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 44 through 48 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.629A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.619A pdb=" N GLU R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER R 49 " --> pdb=" O GLN R 45 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 167 Processing helix chain 'R' and resid 174 through 201 removed outlier: 3.544A pdb=" N LEU R 201 " --> pdb=" O LYS R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 212 No H-bonds generated for 'chain 'R' and resid 210 through 212' Processing helix chain 'R' and resid 213 through 223 removed outlier: 3.814A pdb=" N TYR R 220 " --> pdb=" O GLY R 216 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP R 222 " --> pdb=" O LEU R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 256 Processing helix chain 'R' and resid 261 through 274 removed outlier: 3.766A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 291 removed outlier: 3.692A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.671A pdb=" N VAL R 287 " --> pdb=" O PRO R 283 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR R 289 " --> pdb=" O GLY R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 337 Proline residue: R 312 - end of helix removed outlier: 3.696A pdb=" N LEU R 322 " --> pdb=" O GLY R 318 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER R 333 " --> pdb=" O CYS R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 361 removed outlier: 3.519A pdb=" N LEU R 349 " --> pdb=" O ILE R 345 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 371 removed outlier: 3.819A pdb=" N PHE R 369 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 392 removed outlier: 3.835A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 402 Processing helix chain 'R' and resid 406 through 419 removed outlier: 3.513A pdb=" N TRP R 417 " --> pdb=" O PHE R 413 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG R 419 " --> pdb=" O LYS R 415 " (cutoff:3.500A) Processing helix chain 'R' and resid 420 through 423 removed outlier: 3.651A pdb=" N GLU R 423 " --> pdb=" O TRP R 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 420 through 423' Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.326A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.864A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.093A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.397A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.104A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.679A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.817A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.408A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.728A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 79 through 80 removed outlier: 3.503A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 83 through 84 removed outlier: 4.085A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1299 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: 3.10 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1656 1.27 - 1.40: 2709 1.40 - 1.54: 5847 1.54 - 1.68: 61 1.68 - 1.81: 79 Bond restraints: 10352 Sorted by residual: bond pdb=" C27 UK4 R 501 " pdb=" C28 UK4 R 501 " ideal model delta sigma weight residual 1.535 1.424 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C38 UK4 R 501 " pdb=" C39 UK4 R 501 " ideal model delta sigma weight residual 1.427 1.529 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C PRO A 115 " pdb=" N PRO A 116 " ideal model delta sigma weight residual 1.330 1.381 -0.051 1.19e-02 7.06e+03 1.82e+01 bond pdb=" C ASP B 27 " pdb=" N ALA B 28 " ideal model delta sigma weight residual 1.332 1.383 -0.051 1.25e-02 6.40e+03 1.66e+01 bond pdb=" C PHE A 142 " pdb=" N PRO A 143 " ideal model delta sigma weight residual 1.329 1.377 -0.048 1.18e-02 7.18e+03 1.64e+01 ... (remaining 10347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 13909 3.57 - 7.14: 126 7.14 - 10.70: 8 10.70 - 14.27: 0 14.27 - 17.84: 1 Bond angle restraints: 14044 Sorted by residual: angle pdb=" N ILE A 308 " pdb=" CA ILE A 308 " pdb=" C ILE A 308 " ideal model delta sigma weight residual 112.04 101.46 10.58 1.40e+00 5.10e-01 5.71e+01 angle pdb=" N PRO A 138 " pdb=" CA PRO A 138 " pdb=" C PRO A 138 " ideal model delta sigma weight residual 113.53 103.10 10.43 1.39e+00 5.18e-01 5.63e+01 angle pdb=" C08 UK4 R 501 " pdb=" C09 UK4 R 501 " pdb=" C32 UK4 R 501 " ideal model delta sigma weight residual 110.26 92.42 17.84 3.00e+00 1.11e-01 3.54e+01 angle pdb=" C VAL A 114 " pdb=" N PRO A 115 " pdb=" CA PRO A 115 " ideal model delta sigma weight residual 120.38 125.97 -5.59 1.03e+00 9.43e-01 2.95e+01 angle pdb=" C VAL A 191 " pdb=" N PRO A 192 " pdb=" CA PRO A 192 " ideal model delta sigma weight residual 119.76 125.25 -5.49 1.03e+00 9.43e-01 2.84e+01 ... (remaining 14039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5457 17.47 - 34.95: 518 34.95 - 52.42: 138 52.42 - 69.89: 27 69.89 - 87.36: 13 Dihedral angle restraints: 6153 sinusoidal: 2457 harmonic: 3696 Sorted by residual: dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual 93.00 173.00 -80.00 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CA VAL A 114 " pdb=" C VAL A 114 " pdb=" N PRO A 115 " pdb=" CA PRO A 115 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ASN A 292 " pdb=" C ASN A 292 " pdb=" N LYS A 293 " pdb=" CA LYS A 293 " ideal model delta harmonic sigma weight residual -180.00 -157.75 -22.25 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 6150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1262 0.071 - 0.143: 201 0.143 - 0.214: 55 0.214 - 0.286: 20 0.286 - 0.357: 5 Chirality restraints: 1543 Sorted by residual: chirality pdb=" CA ILE A 308 " pdb=" N ILE A 308 " pdb=" C ILE A 308 " pdb=" CB ILE A 308 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA VAL A 214 " pdb=" N VAL A 214 " pdb=" C VAL A 214 " pdb=" CB VAL A 214 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA LYS A 100 " pdb=" N LYS A 100 " pdb=" C LYS A 100 " pdb=" CB LYS A 100 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 1540 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 364 " -0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C THR A 364 " 0.068 2.00e-02 2.50e+03 pdb=" O THR A 364 " -0.026 2.00e-02 2.50e+03 pdb=" N CYS A 365 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 322 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C GLU A 322 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU A 322 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP A 323 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 61 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C PHE G 61 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE G 61 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG G 62 " 0.014 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 285 2.69 - 3.24: 10042 3.24 - 3.80: 16022 3.80 - 4.35: 22922 4.35 - 4.90: 35848 Nonbonded interactions: 85119 Sorted by model distance: nonbonded pdb=" O THR A 325 " pdb=" OG1 THR A 325 " model vdw 2.140 3.040 nonbonded pdb=" O HOH R 603 " pdb=" O HOH R 617 " model vdw 2.230 3.040 nonbonded pdb=" O GLN R 234 " pdb=" O HOH R 601 " model vdw 2.233 3.040 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR R 152 " pdb=" O HOH R 602 " model vdw 2.261 3.040 ... (remaining 85114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.780 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 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 0.111 10352 Z= 0.374 Angle : 0.926 17.839 14044 Z= 0.655 Chirality : 0.066 0.357 1543 Planarity : 0.004 0.051 1794 Dihedral : 15.442 87.364 3743 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.79 % Allowed : 15.97 % Favored : 80.24 % 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: -3.15 (0.21), residues: 1246 helix: -2.54 (0.18), residues: 498 sheet: -1.43 (0.34), residues: 193 loop : -1.72 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS A 149 PHE 0.012 0.001 PHE A 219 TYR 0.025 0.001 TYR B 145 ARG 0.003 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.2248 (ptt) cc_final: 0.1891 (mtm) REVERT: A 222 PHE cc_start: 0.7406 (m-80) cc_final: 0.7150 (m-80) REVERT: A 265 ARG cc_start: 0.7206 (mtp85) cc_final: 0.6997 (ttt-90) REVERT: A 358 TYR cc_start: 0.6807 (m-80) cc_final: 0.6163 (m-80) REVERT: B 38 ASP cc_start: 0.5869 (OUTLIER) cc_final: 0.5043 (p0) REVERT: B 44 GLN cc_start: 0.6341 (mp10) cc_final: 0.5987 (mp10) REVERT: B 75 GLN cc_start: 0.7394 (mm-40) cc_final: 0.7181 (tp40) REVERT: B 142 HIS cc_start: 0.6783 (OUTLIER) cc_final: 0.5731 (m-70) REVERT: B 228 ASP cc_start: 0.7773 (m-30) cc_final: 0.7539 (m-30) REVERT: B 322 ASP cc_start: 0.5199 (OUTLIER) cc_final: 0.4932 (t70) REVERT: G 32 LYS cc_start: 0.6958 (mmmt) cc_final: 0.6483 (tptt) REVERT: N 43 LYS cc_start: 0.6071 (tmtt) cc_final: 0.5806 (tmtt) REVERT: N 78 THR cc_start: 0.7667 (OUTLIER) cc_final: 0.7367 (m) REVERT: R 62 CYS cc_start: 0.1138 (OUTLIER) cc_final: 0.0588 (m) REVERT: R 67 ASP cc_start: 0.7114 (p0) cc_final: 0.6785 (p0) REVERT: R 170 ARG cc_start: 0.5551 (ttt180) cc_final: 0.5301 (tpp80) REVERT: R 414 ARG cc_start: 0.5815 (mmt-90) cc_final: 0.5337 (mmm160) outliers start: 41 outliers final: 17 residues processed: 197 average time/residue: 1.0459 time to fit residues: 223.7350 Evaluate side-chains 145 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 126 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 0.0050 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN A 64 HIS A 112 ASN A 136 ASN A 170 GLN A 187 GLN A 218 ASN A 236 GLN A 377 ASN A 390 GLN B 16 ASN B 36 ASN B 88 ASN B 110 ASN B 125 ASN B 155 ASN B 176 GLN B 183 HIS B 268 ASN B 295 ASN B 340 ASN G 18 GLN G 24 ASN N 1 GLN N 31 ASN N 77 ASN R 45 GLN R 263 GLN R 304 ASN R 394 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10352 Z= 0.169 Angle : 0.589 10.526 14044 Z= 0.312 Chirality : 0.042 0.146 1543 Planarity : 0.004 0.050 1794 Dihedral : 6.307 59.416 1439 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.80 % Allowed : 16.71 % Favored : 78.49 % 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: -1.40 (0.22), residues: 1246 helix: -0.49 (0.22), residues: 496 sheet: -0.87 (0.33), residues: 218 loop : -1.24 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.005 0.001 HIS A 64 PHE 0.010 0.001 PHE A 212 TYR 0.028 0.002 TYR R 148 ARG 0.008 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 132 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.1707 (ptt) cc_final: 0.1494 (mtm) REVERT: A 265 ARG cc_start: 0.7087 (mtp85) cc_final: 0.6189 (ttt-90) REVERT: A 267 GLN cc_start: 0.7941 (tp-100) cc_final: 0.7720 (tp-100) REVERT: A 358 TYR cc_start: 0.6781 (m-80) cc_final: 0.6063 (m-80) REVERT: B 44 GLN cc_start: 0.6282 (mp10) cc_final: 0.5919 (mp10) REVERT: B 59 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.5823 (t80) REVERT: B 124 TYR cc_start: 0.5426 (m-80) cc_final: 0.5074 (m-80) REVERT: B 142 HIS cc_start: 0.6742 (OUTLIER) cc_final: 0.4839 (m-70) REVERT: B 205 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.7100 (p0) REVERT: B 261 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7696 (mp) REVERT: G 32 LYS cc_start: 0.6953 (mmmt) cc_final: 0.6490 (tptt) REVERT: N 43 LYS cc_start: 0.6131 (tmtt) cc_final: 0.5877 (mmtp) REVERT: N 46 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6646 (mm-30) REVERT: N 89 GLU cc_start: 0.6767 (mp0) cc_final: 0.6387 (mp0) REVERT: R 50 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5326 (mp) REVERT: R 170 ARG cc_start: 0.5542 (ttt180) cc_final: 0.5260 (tpp80) REVERT: R 346 LYS cc_start: 0.5860 (mttp) cc_final: 0.5464 (mtmt) REVERT: R 371 MET cc_start: 0.7759 (tpp) cc_final: 0.7395 (tpp) REVERT: R 411 LEU cc_start: 0.6751 (mt) cc_final: 0.6519 (mt) REVERT: R 414 ARG cc_start: 0.5660 (mmt-90) cc_final: 0.5247 (mmm160) outliers start: 52 outliers final: 28 residues processed: 177 average time/residue: 1.1794 time to fit residues: 225.2403 Evaluate side-chains 143 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 110 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 111 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN A 390 GLN B 110 ASN B 125 ASN B 155 ASN B 268 ASN N 1 GLN N 3 GLN R 45 GLN R 177 ASN R 212 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10352 Z= 0.195 Angle : 0.597 9.082 14044 Z= 0.314 Chirality : 0.043 0.143 1543 Planarity : 0.004 0.056 1794 Dihedral : 5.983 56.852 1424 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.45 % Allowed : 17.91 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.23), residues: 1246 helix: 0.22 (0.23), residues: 492 sheet: -0.60 (0.33), residues: 222 loop : -1.00 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.008 0.001 HIS A 220 PHE 0.013 0.002 PHE A 222 TYR 0.028 0.002 TYR R 148 ARG 0.009 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 119 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7062 (mtp85) cc_final: 0.6129 (ttt-90) REVERT: B 44 GLN cc_start: 0.6298 (mp10) cc_final: 0.5924 (mp10) REVERT: B 59 TYR cc_start: 0.6824 (OUTLIER) cc_final: 0.5845 (t80) REVERT: B 124 TYR cc_start: 0.5416 (m-80) cc_final: 0.5124 (m-80) REVERT: B 142 HIS cc_start: 0.7257 (OUTLIER) cc_final: 0.5693 (m-70) REVERT: B 261 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7742 (mp) REVERT: B 266 HIS cc_start: 0.6030 (t-170) cc_final: 0.5796 (t70) REVERT: G 32 LYS cc_start: 0.7048 (mmmt) cc_final: 0.6545 (tptt) REVERT: N 30 SER cc_start: 0.7952 (OUTLIER) cc_final: 0.7654 (p) REVERT: N 43 LYS cc_start: 0.6103 (tmtt) cc_final: 0.5868 (mmtp) REVERT: N 46 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6663 (mm-30) REVERT: R 50 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5437 (mp) REVERT: R 67 ASP cc_start: 0.7114 (p0) cc_final: 0.6870 (p0) REVERT: R 170 ARG cc_start: 0.5579 (ttt180) cc_final: 0.5340 (tpp80) REVERT: R 346 LYS cc_start: 0.5879 (mttp) cc_final: 0.5510 (mtmt) REVERT: R 371 MET cc_start: 0.7746 (tpp) cc_final: 0.7519 (tpp) REVERT: R 411 LEU cc_start: 0.6819 (mt) cc_final: 0.6542 (mt) REVERT: R 414 ARG cc_start: 0.5624 (mmt-90) cc_final: 0.5348 (mmm160) outliers start: 59 outliers final: 29 residues processed: 168 average time/residue: 0.9867 time to fit residues: 180.9434 Evaluate side-chains 143 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 109 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 293 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN B 110 ASN B 155 ASN B 268 ASN R 45 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10352 Z= 0.150 Angle : 0.545 10.750 14044 Z= 0.284 Chirality : 0.041 0.143 1543 Planarity : 0.004 0.058 1794 Dihedral : 5.819 58.461 1424 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.36 % Allowed : 18.74 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1246 helix: 0.72 (0.24), residues: 488 sheet: -0.50 (0.33), residues: 230 loop : -0.80 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.011 0.001 HIS A 220 PHE 0.015 0.001 PHE A 222 TYR 0.028 0.001 TYR R 148 ARG 0.009 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 113 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7008 (mtp85) cc_final: 0.6067 (ttt-90) REVERT: B 44 GLN cc_start: 0.6274 (mp10) cc_final: 0.5912 (mp10) REVERT: B 59 TYR cc_start: 0.6699 (OUTLIER) cc_final: 0.5739 (t80) REVERT: B 124 TYR cc_start: 0.5389 (m-80) cc_final: 0.5088 (m-80) REVERT: B 142 HIS cc_start: 0.7034 (OUTLIER) cc_final: 0.5663 (m-70) REVERT: B 219 ARG cc_start: 0.6802 (ttm170) cc_final: 0.6527 (ttm110) REVERT: B 261 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7717 (mp) REVERT: B 304 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6067 (mtm180) REVERT: G 32 LYS cc_start: 0.6970 (mmmt) cc_final: 0.6521 (tptt) REVERT: N 1 GLN cc_start: 0.6150 (OUTLIER) cc_final: 0.5636 (pt0) REVERT: N 30 SER cc_start: 0.7892 (OUTLIER) cc_final: 0.7652 (p) REVERT: N 43 LYS cc_start: 0.6234 (tmtt) cc_final: 0.5845 (mmtt) REVERT: N 46 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6620 (mm-30) REVERT: N 78 THR cc_start: 0.7566 (OUTLIER) cc_final: 0.7362 (m) REVERT: N 89 GLU cc_start: 0.6777 (mp0) cc_final: 0.6413 (mp0) REVERT: R 50 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5533 (mp) REVERT: R 52 GLU cc_start: 0.4391 (tm-30) cc_final: 0.3623 (mm-30) REVERT: R 67 ASP cc_start: 0.7021 (p0) cc_final: 0.6772 (p0) REVERT: R 170 ARG cc_start: 0.5520 (ttt180) cc_final: 0.5255 (tpp80) REVERT: R 292 GLU cc_start: 0.5497 (OUTLIER) cc_final: 0.5119 (mt-10) REVERT: R 346 LYS cc_start: 0.5898 (mttp) cc_final: 0.5546 (mtmt) REVERT: R 371 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7370 (tpp) REVERT: R 411 LEU cc_start: 0.6796 (mt) cc_final: 0.6543 (mt) REVERT: R 414 ARG cc_start: 0.5613 (mmt-90) cc_final: 0.5188 (mmm-85) outliers start: 58 outliers final: 30 residues processed: 157 average time/residue: 1.0755 time to fit residues: 183.6165 Evaluate side-chains 146 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 106 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 267 ARG Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 371 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 107 optimal weight: 0.0060 chunk 30 optimal weight: 1.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 155 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10352 Z= 0.175 Angle : 0.574 11.843 14044 Z= 0.301 Chirality : 0.042 0.191 1543 Planarity : 0.004 0.059 1794 Dihedral : 5.974 59.694 1422 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.72 % Allowed : 19.21 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1246 helix: 0.87 (0.24), residues: 486 sheet: -0.49 (0.34), residues: 227 loop : -0.71 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.008 0.001 HIS A 220 PHE 0.012 0.001 PHE B 199 TYR 0.027 0.002 TYR R 148 ARG 0.008 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 109 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.6998 (mtp85) cc_final: 0.6070 (ttt-90) REVERT: B 44 GLN cc_start: 0.6288 (mp10) cc_final: 0.5930 (mp10) REVERT: B 59 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.5772 (t80) REVERT: B 124 TYR cc_start: 0.5431 (m-80) cc_final: 0.5100 (m-80) REVERT: B 142 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.5777 (m-70) REVERT: B 261 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7792 (mp) REVERT: B 304 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6084 (mtm180) REVERT: B 325 MET cc_start: 0.5348 (mmt) cc_final: 0.3710 (ptt) REVERT: G 32 LYS cc_start: 0.6971 (mmmt) cc_final: 0.6492 (tptt) REVERT: N 30 SER cc_start: 0.7930 (OUTLIER) cc_final: 0.7587 (p) REVERT: N 43 LYS cc_start: 0.6205 (tmtt) cc_final: 0.5821 (mmtt) REVERT: N 46 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6631 (mm-30) REVERT: N 78 THR cc_start: 0.7570 (OUTLIER) cc_final: 0.7355 (m) REVERT: N 91 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7367 (t) REVERT: R 50 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5542 (mp) REVERT: R 52 GLU cc_start: 0.4393 (tm-30) cc_final: 0.3628 (mm-30) REVERT: R 67 ASP cc_start: 0.7033 (p0) cc_final: 0.6789 (p0) REVERT: R 170 ARG cc_start: 0.5523 (ttt180) cc_final: 0.5282 (tpp80) REVERT: R 224 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7490 (tt) REVERT: R 292 GLU cc_start: 0.5524 (OUTLIER) cc_final: 0.5122 (mt-10) REVERT: R 346 LYS cc_start: 0.5890 (mttp) cc_final: 0.5533 (mtmt) REVERT: R 371 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7317 (tpp) REVERT: R 389 SER cc_start: 0.6481 (OUTLIER) cc_final: 0.6148 (p) REVERT: R 411 LEU cc_start: 0.6740 (mt) cc_final: 0.6522 (mt) REVERT: R 414 ARG cc_start: 0.5621 (mmt-90) cc_final: 0.5200 (mmm160) outliers start: 62 outliers final: 30 residues processed: 156 average time/residue: 0.9961 time to fit residues: 169.7069 Evaluate side-chains 145 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 103 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 267 ARG Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 371 MET Chi-restraints excluded: chain R residue 389 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 9.9990 chunk 107 optimal weight: 0.0040 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 9 optimal weight: 30.0000 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 110 ASN B 155 ASN B 259 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10352 Z= 0.165 Angle : 0.556 11.028 14044 Z= 0.292 Chirality : 0.041 0.151 1543 Planarity : 0.004 0.056 1794 Dihedral : 5.669 59.728 1420 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.63 % Allowed : 19.67 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1246 helix: 1.00 (0.24), residues: 488 sheet: -0.42 (0.34), residues: 225 loop : -0.62 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 72 HIS 0.004 0.001 HIS A 220 PHE 0.021 0.001 PHE A 376 TYR 0.027 0.002 TYR R 148 ARG 0.009 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 102 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.6990 (mtp85) cc_final: 0.6067 (ttt-90) REVERT: B 44 GLN cc_start: 0.6297 (mp10) cc_final: 0.5951 (mp10) REVERT: B 59 TYR cc_start: 0.6656 (OUTLIER) cc_final: 0.5679 (t80) REVERT: B 124 TYR cc_start: 0.5421 (m-80) cc_final: 0.5077 (m-80) REVERT: B 142 HIS cc_start: 0.6859 (OUTLIER) cc_final: 0.5849 (m-70) REVERT: B 261 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7743 (mp) REVERT: B 304 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6106 (mtm180) REVERT: B 325 MET cc_start: 0.5124 (mmt) cc_final: 0.3842 (ptt) REVERT: G 32 LYS cc_start: 0.6971 (mmmt) cc_final: 0.6473 (tptt) REVERT: N 1 GLN cc_start: 0.6134 (OUTLIER) cc_final: 0.5668 (pt0) REVERT: N 30 SER cc_start: 0.7941 (OUTLIER) cc_final: 0.7575 (p) REVERT: N 43 LYS cc_start: 0.6246 (tmtt) cc_final: 0.5868 (mmtt) REVERT: N 46 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6608 (mm-30) REVERT: N 78 THR cc_start: 0.7558 (OUTLIER) cc_final: 0.7352 (m) REVERT: N 91 THR cc_start: 0.7850 (OUTLIER) cc_final: 0.7350 (t) REVERT: R 50 LEU cc_start: 0.5976 (OUTLIER) cc_final: 0.5580 (mp) REVERT: R 52 GLU cc_start: 0.4331 (tm-30) cc_final: 0.3570 (mm-30) REVERT: R 67 ASP cc_start: 0.6944 (p0) cc_final: 0.6686 (p0) REVERT: R 170 ARG cc_start: 0.5513 (ttt180) cc_final: 0.5256 (tpp80) REVERT: R 292 GLU cc_start: 0.5450 (OUTLIER) cc_final: 0.5020 (mt-10) REVERT: R 346 LYS cc_start: 0.5895 (mttp) cc_final: 0.5544 (OUTLIER) REVERT: R 371 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7328 (tpp) REVERT: R 411 LEU cc_start: 0.6748 (mt) cc_final: 0.6521 (mt) REVERT: R 414 ARG cc_start: 0.5607 (mmt-90) cc_final: 0.5184 (mmm160) outliers start: 61 outliers final: 33 residues processed: 147 average time/residue: 0.9542 time to fit residues: 153.7992 Evaluate side-chains 141 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 98 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 371 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 0.0870 chunk 55 optimal weight: 7.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 155 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10352 Z= 0.181 Angle : 0.570 12.335 14044 Z= 0.299 Chirality : 0.042 0.144 1543 Planarity : 0.004 0.056 1794 Dihedral : 5.726 59.833 1419 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.17 % Allowed : 20.22 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1246 helix: 1.03 (0.24), residues: 486 sheet: -0.49 (0.34), residues: 215 loop : -0.56 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 72 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.002 PHE B 199 TYR 0.027 0.002 TYR R 148 ARG 0.011 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 103 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7587 (mp) REVERT: A 265 ARG cc_start: 0.6990 (mtp85) cc_final: 0.6067 (ttt-90) REVERT: A 376 PHE cc_start: 0.7326 (t80) cc_final: 0.7099 (t80) REVERT: B 44 GLN cc_start: 0.6311 (mp10) cc_final: 0.5968 (mp10) REVERT: B 59 TYR cc_start: 0.6752 (OUTLIER) cc_final: 0.5772 (t80) REVERT: B 142 HIS cc_start: 0.7098 (OUTLIER) cc_final: 0.6457 (m-70) REVERT: B 261 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7775 (mp) REVERT: B 304 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6149 (mtm180) REVERT: B 325 MET cc_start: 0.5139 (mmt) cc_final: 0.4014 (ptt) REVERT: G 32 LYS cc_start: 0.6968 (mmmt) cc_final: 0.6496 (tptt) REVERT: N 43 LYS cc_start: 0.6218 (tmtt) cc_final: 0.5848 (mmtt) REVERT: N 46 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6609 (mm-30) REVERT: N 78 THR cc_start: 0.7570 (OUTLIER) cc_final: 0.7358 (m) REVERT: N 91 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7370 (t) REVERT: R 52 GLU cc_start: 0.4412 (tm-30) cc_final: 0.3627 (mm-30) REVERT: R 67 ASP cc_start: 0.6947 (p0) cc_final: 0.6684 (p0) REVERT: R 170 ARG cc_start: 0.5550 (ttt180) cc_final: 0.5287 (tpp80) REVERT: R 292 GLU cc_start: 0.5422 (OUTLIER) cc_final: 0.4969 (mt-10) REVERT: R 346 LYS cc_start: 0.5860 (mttp) cc_final: 0.5523 (OUTLIER) REVERT: R 371 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7434 (tpp) REVERT: R 411 LEU cc_start: 0.6748 (mt) cc_final: 0.6531 (mt) REVERT: R 414 ARG cc_start: 0.5690 (mmt-90) cc_final: 0.5247 (mmm160) outliers start: 56 outliers final: 34 residues processed: 148 average time/residue: 0.9850 time to fit residues: 159.1147 Evaluate side-chains 140 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 98 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 371 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 155 ASN B 259 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10352 Z= 0.153 Angle : 0.547 11.567 14044 Z= 0.287 Chirality : 0.041 0.144 1543 Planarity : 0.004 0.055 1794 Dihedral : 5.577 59.301 1419 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.99 % Allowed : 21.24 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.24), residues: 1246 helix: 1.13 (0.24), residues: 490 sheet: -0.37 (0.34), residues: 227 loop : -0.55 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 72 HIS 0.003 0.001 HIS A 220 PHE 0.011 0.001 PHE B 199 TYR 0.027 0.001 TYR R 148 ARG 0.011 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 103 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7586 (mp) REVERT: A 265 ARG cc_start: 0.6975 (mtp85) cc_final: 0.6050 (ttt-90) REVERT: B 44 GLN cc_start: 0.6305 (mp10) cc_final: 0.5965 (mp10) REVERT: B 59 TYR cc_start: 0.6639 (OUTLIER) cc_final: 0.5631 (t80) REVERT: B 142 HIS cc_start: 0.6969 (OUTLIER) cc_final: 0.6177 (m-70) REVERT: B 261 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7739 (mp) REVERT: B 304 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6175 (mtm180) REVERT: B 325 MET cc_start: 0.5223 (mmt) cc_final: 0.4263 (ptt) REVERT: G 32 LYS cc_start: 0.6954 (mmmt) cc_final: 0.6481 (tptt) REVERT: N 30 SER cc_start: 0.7947 (OUTLIER) cc_final: 0.7588 (p) REVERT: N 43 LYS cc_start: 0.6228 (tmtt) cc_final: 0.5840 (mmtt) REVERT: N 46 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6592 (mm-30) REVERT: N 65 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6475 (mtpt) REVERT: N 78 THR cc_start: 0.7557 (OUTLIER) cc_final: 0.7352 (m) REVERT: N 91 THR cc_start: 0.7829 (OUTLIER) cc_final: 0.7339 (t) REVERT: R 50 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5578 (mp) REVERT: R 52 GLU cc_start: 0.4355 (tm-30) cc_final: 0.3605 (mm-30) REVERT: R 67 ASP cc_start: 0.6911 (p0) cc_final: 0.6640 (p0) REVERT: R 170 ARG cc_start: 0.5465 (ttt180) cc_final: 0.5217 (tpp80) REVERT: R 224 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7495 (tt) REVERT: R 346 LYS cc_start: 0.5858 (mttp) cc_final: 0.5539 (mtmt) REVERT: R 371 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7435 (tpp) REVERT: R 411 LEU cc_start: 0.6732 (mt) cc_final: 0.6524 (mt) REVERT: R 414 ARG cc_start: 0.5640 (mmt-90) cc_final: 0.5252 (mmm160) outliers start: 54 outliers final: 30 residues processed: 146 average time/residue: 1.0007 time to fit residues: 159.4077 Evaluate side-chains 138 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 96 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 371 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 0.0980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 155 ASN B 220 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10352 Z= 0.151 Angle : 0.545 11.505 14044 Z= 0.286 Chirality : 0.041 0.141 1543 Planarity : 0.004 0.054 1794 Dihedral : 5.494 58.454 1419 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.16 % Allowed : 21.88 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1246 helix: 1.24 (0.24), residues: 490 sheet: -0.33 (0.34), residues: 227 loop : -0.50 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 72 HIS 0.003 0.001 HIS B 266 PHE 0.021 0.001 PHE A 376 TYR 0.028 0.001 TYR R 148 ARG 0.013 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 101 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6486 (mmm160) cc_final: 0.6057 (mmt180) REVERT: A 46 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7551 (mp) REVERT: A 135 MET cc_start: 0.1432 (mtm) cc_final: 0.1139 (pp-130) REVERT: A 265 ARG cc_start: 0.6965 (mtp85) cc_final: 0.6039 (ttt-90) REVERT: B 44 GLN cc_start: 0.6356 (mp10) cc_final: 0.6031 (mp10) REVERT: B 59 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.5855 (t80) REVERT: B 142 HIS cc_start: 0.7010 (OUTLIER) cc_final: 0.6471 (m-70) REVERT: B 261 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7720 (mp) REVERT: B 304 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6173 (mtm180) REVERT: B 325 MET cc_start: 0.5092 (mmt) cc_final: 0.4250 (ptt) REVERT: G 32 LYS cc_start: 0.7081 (mmmt) cc_final: 0.6649 (tptt) REVERT: N 30 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7590 (p) REVERT: N 43 LYS cc_start: 0.6244 (tmtt) cc_final: 0.5860 (mmtt) REVERT: N 46 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6602 (mm-30) REVERT: N 65 LYS cc_start: 0.6827 (OUTLIER) cc_final: 0.6513 (mtpt) REVERT: N 91 THR cc_start: 0.7849 (OUTLIER) cc_final: 0.7346 (t) REVERT: R 50 LEU cc_start: 0.5949 (OUTLIER) cc_final: 0.5633 (mp) REVERT: R 52 GLU cc_start: 0.4283 (tm-30) cc_final: 0.3604 (mm-30) REVERT: R 67 ASP cc_start: 0.6893 (p0) cc_final: 0.6609 (p0) REVERT: R 93 SER cc_start: 0.6287 (OUTLIER) cc_final: 0.6023 (p) REVERT: R 170 ARG cc_start: 0.5495 (ttt180) cc_final: 0.5247 (tpp80) REVERT: R 224 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7464 (tt) REVERT: R 346 LYS cc_start: 0.5805 (mttp) cc_final: 0.5490 (mtmt) REVERT: R 371 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7579 (tpp) REVERT: R 411 LEU cc_start: 0.6807 (mt) cc_final: 0.6605 (mt) REVERT: R 414 ARG cc_start: 0.5610 (mmt-90) cc_final: 0.5239 (mmm160) outliers start: 45 outliers final: 26 residues processed: 135 average time/residue: 0.9732 time to fit residues: 144.0597 Evaluate side-chains 137 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 99 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 371 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.2980 chunk 71 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 155 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10352 Z= 0.279 Angle : 0.664 13.349 14044 Z= 0.351 Chirality : 0.046 0.168 1543 Planarity : 0.005 0.058 1794 Dihedral : 6.091 58.079 1419 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.43 % Allowed : 21.98 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1246 helix: 0.78 (0.23), residues: 485 sheet: -0.41 (0.33), residues: 231 loop : -0.67 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 82 HIS 0.006 0.002 HIS B 311 PHE 0.024 0.002 PHE A 222 TYR 0.031 0.003 TYR R 148 ARG 0.012 0.001 ARG A 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 100 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.4735 (mtm-85) cc_final: 0.3308 (ptt180) REVERT: A 265 ARG cc_start: 0.7036 (mtp85) cc_final: 0.6111 (ttt-90) REVERT: A 376 PHE cc_start: 0.7325 (t80) cc_final: 0.7057 (t80) REVERT: B 44 GLN cc_start: 0.6310 (mp10) cc_final: 0.5966 (mp10) REVERT: B 59 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.5897 (t80) REVERT: B 82 TRP cc_start: 0.3458 (m100) cc_final: 0.3220 (t-100) REVERT: B 142 HIS cc_start: 0.7265 (OUTLIER) cc_final: 0.6049 (m-70) REVERT: B 261 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7802 (mp) REVERT: B 325 MET cc_start: 0.5093 (mmt) cc_final: 0.4184 (ptt) REVERT: G 32 LYS cc_start: 0.6954 (mmmt) cc_final: 0.6539 (tptt) REVERT: N 43 LYS cc_start: 0.6243 (tmtt) cc_final: 0.5882 (mmtt) REVERT: N 46 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6694 (mm-30) REVERT: R 50 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5470 (mp) REVERT: R 67 ASP cc_start: 0.7027 (p0) cc_final: 0.6774 (p0) REVERT: R 170 ARG cc_start: 0.5545 (ttt180) cc_final: 0.5284 (tpp80) REVERT: R 224 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7643 (tt) REVERT: R 346 LYS cc_start: 0.5854 (mttp) cc_final: 0.5525 (mtmt) REVERT: R 371 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7415 (tpp) REVERT: R 397 MET cc_start: 0.6555 (mmt) cc_final: 0.6351 (mmp) REVERT: R 411 LEU cc_start: 0.6762 (mt) cc_final: 0.6539 (mt) REVERT: R 414 ARG cc_start: 0.5654 (mmt-90) cc_final: 0.5229 (mmm-85) outliers start: 48 outliers final: 30 residues processed: 138 average time/residue: 0.9351 time to fit residues: 141.8232 Evaluate side-chains 133 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 97 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 371 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 18 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 125 ASN B 155 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.223193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.184853 restraints weight = 11216.484| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.39 r_work: 0.3976 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3885 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10352 Z= 0.153 Angle : 0.567 12.208 14044 Z= 0.298 Chirality : 0.042 0.151 1543 Planarity : 0.004 0.055 1794 Dihedral : 5.680 59.875 1419 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.32 % Allowed : 23.27 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1246 helix: 1.09 (0.24), residues: 489 sheet: -0.36 (0.34), residues: 222 loop : -0.60 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 72 HIS 0.003 0.001 HIS B 266 PHE 0.022 0.001 PHE A 222 TYR 0.030 0.001 TYR R 148 ARG 0.014 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3758.37 seconds wall clock time: 70 minutes 58.08 seconds (4258.08 seconds total)