Starting phenix.real_space_refine on Sun Aug 4 20:08:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4i_30986/08_2024/7e4i_30986.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4i_30986/08_2024/7e4i_30986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4i_30986/08_2024/7e4i_30986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4i_30986/08_2024/7e4i_30986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4i_30986/08_2024/7e4i_30986.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4i_30986/08_2024/7e4i_30986.cif" } resolution = 3.05 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= 0.001 sd= 0.116 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 7240 2.51 5 N 1932 2.21 5 O 2117 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3494 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 17, 'TRANS': 421} Chain breaks: 2 Chain: "B" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2536 Classifications: {'peptide': 317} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 307} Chain: "C" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 284} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2378 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Chain: "E" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 317 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "F" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Time building chain proxies: 6.31, per 1000 atoms: 0.56 Number of scatterers: 11336 At special positions: 0 Unit cell: (123.918, 113.048, 115.222, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 2117 8.00 N 1932 7.00 C 7240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 2.0 seconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2680 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 38.5% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 43 through 56 removed outlier: 4.030A pdb=" N ALA A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.764A pdb=" N SER A 268 " --> pdb=" O GLY A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.750A pdb=" N GLN A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.571A pdb=" N LYS A 356 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 removed outlier: 4.174A pdb=" N GLU A 404 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 30 through 37 removed outlier: 3.733A pdb=" N ALA B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 119 through 123 removed outlier: 3.948A pdb=" N ASN B 123 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.509A pdb=" N LEU B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 182 Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.742A pdb=" N GLU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 225 removed outlier: 3.639A pdb=" N VAL B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N SER B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.930A pdb=" N GLY B 243 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 273 removed outlier: 3.725A pdb=" N ASN B 253 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 297 Processing helix chain 'B' and resid 303 through 312 Processing helix chain 'B' and resid 313 through 325 removed outlier: 3.620A pdb=" N VAL B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.669A pdb=" N ILE C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.760A pdb=" N SER C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 4.001A pdb=" N LEU C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 83 removed outlier: 3.505A pdb=" N LYS C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 107 through 132 removed outlier: 3.601A pdb=" N GLU C 111 " --> pdb=" O ASP C 107 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ARG C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 126 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.954A pdb=" N LEU C 144 " --> pdb=" O TYR C 140 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.608A pdb=" N TRP C 154 " --> pdb=" O PHE C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.867A pdb=" N LEU C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 241 removed outlier: 4.155A pdb=" N GLY C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 223 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 263 removed outlier: 3.555A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 removed outlier: 4.180A pdb=" N ILE C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 314 through 327 removed outlier: 3.526A pdb=" N TYR C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 Processing helix chain 'D' and resid 62 through 66 removed outlier: 3.879A pdb=" N LEU D 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 364 through 373 Processing helix chain 'E' and resid 14 through 49 Proline residue: E 39 - end of helix Processing helix chain 'F' and resid 30 through 51 Processing helix chain 'F' and resid 51 through 58 removed outlier: 3.837A pdb=" N ASP F 55 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA F 58 " --> pdb=" O MET F 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 37 removed outlier: 5.042A pdb=" N VAL A 31 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL A 112 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY A 33 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLN A 114 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 35 " --> pdb=" O GLN A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 132 removed outlier: 3.780A pdb=" N ASP A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE A 168 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN A 196 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 180 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 414 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 466 removed outlier: 7.092A pdb=" N ALA A 465 " --> pdb=" O TYR B 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 43 removed outlier: 6.282A pdb=" N TYR B 60 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU B 116 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU B 62 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.576A pdb=" N THR B 45 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 47 removed outlier: 5.921A pdb=" N VAL C 6 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 83 through 93 removed outlier: 6.839A pdb=" N PHE D 98 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N CYS D 165 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR D 194 " --> pdb=" O PRO D 185 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D 205 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU D 209 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLY D 83 " --> pdb=" O CYS D 355 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU D 357 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG D 85 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N PHE D 359 " --> pdb=" O ARG D 85 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP D 87 " --> pdb=" O PHE D 359 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR D 361 " --> pdb=" O ASP D 87 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASN D 89 " --> pdb=" O THR D 361 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1776 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: 3.33 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3662 1.34 - 1.46: 2389 1.46 - 1.58: 5443 1.58 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 11565 Sorted by residual: bond pdb=" CG PRO B 19 " pdb=" CD PRO B 19 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.70e-02 1.37e+03 8.19e-01 bond pdb=" CB PRO B 129 " pdb=" CG PRO B 129 " ideal model delta sigma weight residual 1.506 1.477 0.029 3.90e-02 6.57e+02 5.66e-01 bond pdb=" CA PRO B 302 " pdb=" C PRO B 302 " ideal model delta sigma weight residual 1.527 1.519 0.008 1.07e-02 8.73e+03 5.33e-01 bond pdb=" C LEU C 60 " pdb=" N PRO C 61 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.09e-01 bond pdb=" CA ILE A 117 " pdb=" C ILE A 117 " ideal model delta sigma weight residual 1.517 1.527 -0.010 1.49e-02 4.50e+03 4.55e-01 ... (remaining 11560 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.85: 261 106.85 - 113.64: 6412 113.64 - 120.43: 4313 120.43 - 127.22: 4529 127.22 - 134.00: 116 Bond angle restraints: 15631 Sorted by residual: angle pdb=" N ILE B 154 " pdb=" CA ILE B 154 " pdb=" C ILE B 154 " ideal model delta sigma weight residual 113.20 109.44 3.76 9.60e-01 1.09e+00 1.53e+01 angle pdb=" N THR A 294 " pdb=" CA THR A 294 " pdb=" C THR A 294 " ideal model delta sigma weight residual 114.56 110.03 4.53 1.27e+00 6.20e-01 1.27e+01 angle pdb=" C ASP A 53 " pdb=" N THR A 54 " pdb=" CA THR A 54 " ideal model delta sigma weight residual 122.53 116.79 5.74 1.92e+00 2.71e-01 8.94e+00 angle pdb=" CA THR A 294 " pdb=" C THR A 294 " pdb=" N LYS A 295 " ideal model delta sigma weight residual 119.26 116.73 2.53 1.14e+00 7.69e-01 4.94e+00 angle pdb=" CA LEU C 60 " pdb=" C LEU C 60 " pdb=" N PRO C 61 " ideal model delta sigma weight residual 118.44 121.74 -3.30 1.59e+00 3.96e-01 4.30e+00 ... (remaining 15626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 6610 16.48 - 32.97: 247 32.97 - 49.45: 52 49.45 - 65.93: 15 65.93 - 82.41: 4 Dihedral angle restraints: 6928 sinusoidal: 2786 harmonic: 4142 Sorted by residual: dihedral pdb=" CA LYS C 59 " pdb=" C LYS C 59 " pdb=" N LEU C 60 " pdb=" CA LEU C 60 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ASN D 95 " pdb=" C ASN D 95 " pdb=" N PRO D 96 " pdb=" CA PRO D 96 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TRP A 197 " pdb=" C TRP A 197 " pdb=" N ASN A 198 " pdb=" CA ASN A 198 " ideal model delta harmonic sigma weight residual 180.00 -162.75 -17.25 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 6925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1041 0.028 - 0.057: 508 0.057 - 0.085: 122 0.085 - 0.113: 76 0.113 - 0.142: 17 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CA ILE D 256 " pdb=" N ILE D 256 " pdb=" C ILE D 256 " pdb=" CB ILE D 256 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA LEU C 60 " pdb=" N LEU C 60 " pdb=" C LEU C 60 " pdb=" CB LEU C 60 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE C 64 " pdb=" N ILE C 64 " pdb=" C ILE C 64 " pdb=" CB ILE C 64 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 1761 not shown) Planarity restraints: 1988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 206 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO D 207 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 207 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 207 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 52 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C ASP A 52 " -0.022 2.00e-02 2.50e+03 pdb=" O ASP A 52 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP A 53 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 258 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 259 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " 0.016 5.00e-02 4.00e+02 ... (remaining 1985 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1081 2.75 - 3.29: 10493 3.29 - 3.82: 17349 3.82 - 4.36: 21160 4.36 - 4.90: 37928 Nonbonded interactions: 88011 Sorted by model distance: nonbonded pdb=" OD2 ASP A 288 " pdb=" OG1 THR A 294 " model vdw 2.212 3.040 nonbonded pdb=" OG SER B 184 " pdb=" OE2 GLU B 301 " model vdw 2.241 3.040 nonbonded pdb=" OG SER D 93 " pdb=" O PRO D 96 " model vdw 2.248 3.040 nonbonded pdb=" OG SER A 344 " pdb=" O SER A 348 " model vdw 2.259 3.040 nonbonded pdb=" O SER A 253 " pdb=" OH TYR A 262 " model vdw 2.292 3.040 ... (remaining 88006 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 31.720 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.002 0.029 11565 Z= 0.134 Angle : 0.483 6.606 15631 Z= 0.271 Chirality : 0.039 0.142 1764 Planarity : 0.003 0.043 1988 Dihedral : 9.900 82.414 4248 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.42 % Allowed : 4.59 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.19 (0.23), residues: 1404 helix: 0.78 (0.26), residues: 450 sheet: 0.50 (0.25), residues: 442 loop : -0.68 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 240 HIS 0.003 0.001 HIS A 310 PHE 0.015 0.001 PHE A 237 TYR 0.011 0.001 TYR B 164 ARG 0.002 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7573 (m170) cc_final: 0.7272 (m170) REVERT: A 456 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7342 (mt-10) REVERT: B 17 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7625 (t) REVERT: B 135 TYR cc_start: 0.8707 (t80) cc_final: 0.8463 (t80) REVERT: B 168 ASP cc_start: 0.8219 (p0) cc_final: 0.7997 (p0) REVERT: B 205 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7554 (tp) REVERT: B 251 SER cc_start: 0.8721 (t) cc_final: 0.8461 (t) REVERT: D 94 MET cc_start: 0.6368 (mmp) cc_final: 0.5866 (ptm) REVERT: D 186 SER cc_start: 0.6028 (t) cc_final: 0.5788 (m) REVERT: D 267 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8023 (m) REVERT: D 369 MET cc_start: 0.4132 (mtt) cc_final: 0.3512 (mmm) outliers start: 18 outliers final: 6 residues processed: 176 average time/residue: 0.2352 time to fit residues: 58.6844 Evaluate side-chains 132 residues out of total 1265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 339 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 30.0000 chunk 105 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 159 ASN C 168 ASN C 285 ASN C 300 ASN D 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11565 Z= 0.210 Angle : 0.512 6.459 15631 Z= 0.271 Chirality : 0.041 0.151 1764 Planarity : 0.003 0.044 1988 Dihedral : 5.109 55.428 1528 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.74 % Allowed : 7.52 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1404 helix: 1.18 (0.25), residues: 458 sheet: 0.62 (0.25), residues: 435 loop : -0.75 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 240 HIS 0.004 0.001 HIS A 238 PHE 0.019 0.001 PHE D 340 TYR 0.018 0.001 TYR A 140 ARG 0.003 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7606 (mmtt) REVERT: A 169 HIS cc_start: 0.7844 (m170) cc_final: 0.7504 (m170) REVERT: A 298 MET cc_start: 0.8502 (tmm) cc_final: 0.7801 (tmm) REVERT: A 299 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8581 (tp) REVERT: B 17 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7674 (t) REVERT: B 135 TYR cc_start: 0.8740 (t80) cc_final: 0.8442 (t80) REVERT: B 205 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7345 (tp) REVERT: C 153 MET cc_start: 0.8513 (mtm) cc_final: 0.8124 (mpp) REVERT: D 94 MET cc_start: 0.6342 (mmp) cc_final: 0.5815 (ptm) REVERT: D 186 SER cc_start: 0.6317 (t) cc_final: 0.6047 (m) REVERT: D 369 MET cc_start: 0.4271 (mtt) cc_final: 0.3630 (mmm) outliers start: 22 outliers final: 13 residues processed: 141 average time/residue: 0.2331 time to fit residues: 47.0330 Evaluate side-chains 132 residues out of total 1265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 339 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11565 Z= 0.273 Angle : 0.535 7.433 15631 Z= 0.283 Chirality : 0.042 0.168 1764 Planarity : 0.004 0.044 1988 Dihedral : 5.027 53.001 1524 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.22 % Allowed : 7.99 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.23), residues: 1404 helix: 1.19 (0.25), residues: 463 sheet: 0.64 (0.25), residues: 431 loop : -0.76 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 9 HIS 0.006 0.001 HIS A 310 PHE 0.015 0.001 PHE B 44 TYR 0.023 0.001 TYR A 140 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7853 (m170) cc_final: 0.7543 (m170) REVERT: A 298 MET cc_start: 0.8468 (tmm) cc_final: 0.7785 (tmm) REVERT: A 299 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8634 (tp) REVERT: B 17 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7679 (t) REVERT: B 135 TYR cc_start: 0.8799 (t80) cc_final: 0.8488 (t80) REVERT: B 205 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7181 (tp) REVERT: C 153 MET cc_start: 0.8559 (mtm) cc_final: 0.8120 (mpp) REVERT: C 271 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8106 (mp) REVERT: D 70 VAL cc_start: 0.6898 (OUTLIER) cc_final: 0.6651 (p) REVERT: D 94 MET cc_start: 0.6347 (mmp) cc_final: 0.5829 (ptm) REVERT: D 369 MET cc_start: 0.4135 (mtt) cc_final: 0.3502 (mmm) outliers start: 28 outliers final: 19 residues processed: 142 average time/residue: 0.2341 time to fit residues: 47.8293 Evaluate side-chains 142 residues out of total 1265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 339 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 84 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 120 optimal weight: 30.0000 chunk 36 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN C 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11565 Z= 0.264 Angle : 0.528 7.394 15631 Z= 0.279 Chirality : 0.041 0.171 1764 Planarity : 0.003 0.050 1988 Dihedral : 5.057 51.831 1524 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.53 % Allowed : 8.47 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1404 helix: 1.25 (0.25), residues: 464 sheet: 0.62 (0.25), residues: 429 loop : -0.84 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 240 HIS 0.006 0.001 HIS A 310 PHE 0.021 0.001 PHE D 340 TYR 0.018 0.001 TYR B 164 ARG 0.003 0.000 ARG C 305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 118 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7865 (m170) cc_final: 0.7586 (m170) REVERT: A 298 MET cc_start: 0.8433 (tmm) cc_final: 0.7821 (tmm) REVERT: A 323 TRP cc_start: 0.7910 (OUTLIER) cc_final: 0.7670 (m-90) REVERT: B 135 TYR cc_start: 0.8776 (t80) cc_final: 0.8463 (t80) REVERT: B 205 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7080 (tp) REVERT: C 153 MET cc_start: 0.8562 (mtm) cc_final: 0.8137 (mpp) REVERT: C 271 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8125 (mp) REVERT: D 70 VAL cc_start: 0.6926 (OUTLIER) cc_final: 0.6672 (p) REVERT: D 94 MET cc_start: 0.6387 (mmp) cc_final: 0.5876 (ptm) REVERT: D 272 GLU cc_start: 0.7344 (tp30) cc_final: 0.7123 (tp30) REVERT: D 369 MET cc_start: 0.4141 (mtt) cc_final: 0.3498 (mmm) outliers start: 32 outliers final: 20 residues processed: 144 average time/residue: 0.2344 time to fit residues: 49.0354 Evaluate side-chains 139 residues out of total 1265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 339 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.6363 > 50: distance: 13 - 45: 35.972 distance: 16 - 42: 19.017 distance: 27 - 36: 3.775 distance: 36 - 37: 23.383 distance: 36 - 97: 22.934 distance: 37 - 38: 9.103 distance: 37 - 40: 14.460 distance: 38 - 39: 7.342 distance: 38 - 42: 11.568 distance: 39 - 94: 18.402 distance: 40 - 41: 20.780 distance: 42 - 43: 14.254 distance: 43 - 44: 22.363 distance: 43 - 46: 32.730 distance: 44 - 45: 20.369 distance: 44 - 53: 24.965 distance: 46 - 47: 17.438 distance: 47 - 48: 9.994 distance: 48 - 49: 8.238 distance: 49 - 50: 6.253 distance: 50 - 51: 6.131 distance: 50 - 52: 6.029 distance: 53 - 54: 11.823 distance: 54 - 55: 10.807 distance: 54 - 57: 6.995 distance: 55 - 56: 15.689 distance: 55 - 60: 18.824 distance: 57 - 58: 8.956 distance: 57 - 59: 25.283 distance: 60 - 61: 17.329 distance: 61 - 62: 11.635 distance: 61 - 64: 16.053 distance: 62 - 63: 11.853 distance: 62 - 68: 9.975 distance: 64 - 65: 24.020 distance: 65 - 66: 15.988 distance: 65 - 67: 22.715 distance: 68 - 69: 10.920 distance: 69 - 70: 18.808 distance: 70 - 71: 15.131 distance: 70 - 72: 10.130 distance: 72 - 73: 46.430 distance: 73 - 74: 10.203 distance: 73 - 76: 22.600 distance: 74 - 75: 46.507 distance: 74 - 78: 22.428 distance: 76 - 77: 29.766 distance: 78 - 79: 15.221 distance: 79 - 80: 20.720 distance: 79 - 82: 18.429 distance: 80 - 81: 15.845 distance: 80 - 83: 14.592 distance: 83 - 84: 12.664 distance: 83 - 89: 17.577 distance: 84 - 85: 12.926 distance: 84 - 87: 28.813 distance: 85 - 86: 29.402 distance: 85 - 90: 22.765 distance: 87 - 88: 11.358 distance: 88 - 89: 40.596 distance: 90 - 91: 32.370 distance: 91 - 92: 18.159 distance: 92 - 93: 31.920 distance: 92 - 94: 22.447 distance: 94 - 95: 23.938 distance: 95 - 96: 14.057 distance: 95 - 98: 18.683 distance: 96 - 97: 29.811 distance: 96 - 102: 11.436 distance: 98 - 99: 21.858 distance: 99 - 100: 19.693 distance: 99 - 101: 23.806