Starting phenix.real_space_refine on Fri Mar 14 01:25:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jit_36327/03_2025/8jit_36327_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jit_36327/03_2025/8jit_36327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jit_36327/03_2025/8jit_36327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jit_36327/03_2025/8jit_36327.map" model { file = "/net/cci-nas-00/data/ceres_data/8jit_36327/03_2025/8jit_36327_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jit_36327/03_2025/8jit_36327_neut_trim.cif" } resolution = 2.91 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= 0.020 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 56 5.16 5 C 5836 2.51 5 N 1617 2.21 5 O 1684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9193 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1868 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 233 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2574 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 420 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3108 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.80, per 1000 atoms: 0.74 Number of scatterers: 9193 At special positions: 0 Unit cell: (77.112, 99.603, 175.644, 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 56 16.00 O 1684 8.00 N 1617 7.00 C 5836 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=2.05 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.03 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.03 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.0 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 42.3% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 3 through 34 removed outlier: 3.806A pdb=" N ASN A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.625A pdb=" N ILE A 50 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.641A pdb=" N GLN A 220 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS A 221 " --> pdb=" O TRP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.658A pdb=" N TYR A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.520A pdb=" N ARG A 301 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 336 removed outlier: 4.511A pdb=" N SER A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 375 removed outlier: 4.191A pdb=" N ASN A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.755A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.621A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'C' and resid 8 through 21 removed outlier: 4.099A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.855A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.786A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 49 removed outlier: 3.773A pdb=" N LEU R 49 " --> pdb=" O HIS R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'R' and resid 126 through 165 removed outlier: 3.757A pdb=" N VAL R 130 " --> pdb=" O GLU R 126 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU R 158 " --> pdb=" O GLY R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 202 removed outlier: 3.583A pdb=" N ASN R 179 " --> pdb=" O ALA R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 217 Processing helix chain 'R' and resid 220 through 255 removed outlier: 3.787A pdb=" N CYS R 224 " --> pdb=" O ALA R 220 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR R 239 " --> pdb=" O ILE R 235 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU R 255 " --> pdb=" O ASN R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 272 Processing helix chain 'R' and resid 273 through 289 removed outlier: 3.822A pdb=" N LEU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 300 through 303 Processing helix chain 'R' and resid 304 through 317 Proline residue: R 310 - end of helix Processing helix chain 'R' and resid 318 through 334 Processing helix chain 'R' and resid 343 through 354 removed outlier: 3.837A pdb=" N THR R 351 " --> pdb=" O LEU R 347 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU R 352 " --> pdb=" O ALA R 348 " (cutoff:3.500A) Processing helix chain 'R' and resid 374 through 402 removed outlier: 3.566A pdb=" N ARG R 378 " --> pdb=" O GLN R 374 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 420 removed outlier: 3.966A pdb=" N LEU R 420 " --> pdb=" O HIS R 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 198 removed outlier: 6.823A pdb=" N HIS A 35 " --> pdb=" O HIS A 204 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE A 206 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 37 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ARG A 36 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE A 229 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU A 38 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL A 231 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 40 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ALA A 233 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.644A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.565A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.712A 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: 5.721A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.613A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.917A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.527A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.803A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (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 11 through 12 removed outlier: 6.895A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 75 through 80 453 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1902 1.33 - 1.45: 2394 1.45 - 1.57: 5025 1.57 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9397 Sorted by residual: bond pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 1.247 1.341 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C04 D6M P 101 " pdb=" C09 D6M P 101 " ideal model delta sigma weight residual 1.550 1.486 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C THR A 309 " pdb=" N PRO A 310 " ideal model delta sigma weight residual 1.329 1.367 -0.037 1.22e-02 6.72e+03 9.28e+00 bond pdb=" CA THR N 111 " pdb=" C THR N 111 " ideal model delta sigma weight residual 1.529 1.487 0.042 1.40e-02 5.10e+03 9.01e+00 bond pdb=" CA CYS N 99 " pdb=" C CYS N 99 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.02e-02 9.61e+03 8.85e+00 ... (remaining 9392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 12684 4.22 - 8.45: 55 8.45 - 12.67: 3 12.67 - 16.90: 0 16.90 - 21.12: 1 Bond angle restraints: 12743 Sorted by residual: angle pdb=" C06 D6M P 101 " pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 118.04 96.92 21.12 3.00e+00 1.11e-01 4.96e+01 angle pdb=" N ASP N 109 " pdb=" CA ASP N 109 " pdb=" C ASP N 109 " ideal model delta sigma weight residual 113.30 122.71 -9.41 1.34e+00 5.57e-01 4.93e+01 angle pdb=" C THR A 309 " pdb=" N PRO A 310 " pdb=" CA PRO A 310 " ideal model delta sigma weight residual 120.66 113.02 7.64 1.09e+00 8.42e-01 4.92e+01 angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.38 105.27 8.11 1.23e+00 6.61e-01 4.34e+01 angle pdb=" N TRP P 25 " pdb=" CA TRP P 25 " pdb=" C TRP P 25 " ideal model delta sigma weight residual 111.71 105.02 6.69 1.15e+00 7.56e-01 3.39e+01 ... (remaining 12738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5005 17.83 - 35.66: 430 35.66 - 53.48: 94 53.48 - 71.31: 23 71.31 - 89.14: 10 Dihedral angle restraints: 5562 sinusoidal: 2156 harmonic: 3406 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -14.49 -71.51 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" N ASN C 59 " pdb=" C ASN C 59 " pdb=" CA ASN C 59 " pdb=" CB ASN C 59 " ideal model delta harmonic sigma weight residual 122.80 133.65 -10.85 0 2.50e+00 1.60e-01 1.88e+01 dihedral pdb=" C ASN C 59 " pdb=" N ASN C 59 " pdb=" CA ASN C 59 " pdb=" CB ASN C 59 " ideal model delta harmonic sigma weight residual -122.60 -132.44 9.84 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 5559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1319 0.095 - 0.191: 85 0.191 - 0.286: 7 0.286 - 0.381: 1 0.381 - 0.477: 2 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA ASN C 59 " pdb=" N ASN C 59 " pdb=" C ASN C 59 " pdb=" CB ASN C 59 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CB VAL R 212 " pdb=" CA VAL R 212 " pdb=" CG1 VAL R 212 " pdb=" CG2 VAL R 212 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 1411 not shown) Planarity restraints: 1634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER N 25 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C SER N 25 " -0.049 2.00e-02 2.50e+03 pdb=" O SER N 25 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY N 26 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 355 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO R 356 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO R 356 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 356 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 274 " 0.035 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO R 275 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 275 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 275 " 0.030 5.00e-02 4.00e+02 ... (remaining 1631 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1110 2.74 - 3.28: 9587 3.28 - 3.82: 15650 3.82 - 4.36: 18095 4.36 - 4.90: 30824 Nonbonded interactions: 75266 Sorted by model distance: nonbonded pdb=" O ALA R 175 " pdb=" ND2 ASN R 179 " model vdw 2.204 3.120 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.223 3.040 nonbonded pdb=" O TYR A 302 " pdb=" NH2 ARG A 320 " model vdw 2.260 3.120 nonbonded pdb=" O ARG B 22 " pdb=" NH1 ARG B 22 " model vdw 2.263 3.120 nonbonded pdb=" OE1 GLN P 3 " pdb=" OH TYR R 149 " model vdw 2.269 3.040 ... (remaining 75261 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.540 Find NCS groups from input model: 0.140 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:14.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 9397 Z= 0.362 Angle : 0.786 21.123 12743 Z= 0.498 Chirality : 0.052 0.477 1414 Planarity : 0.004 0.065 1634 Dihedral : 14.715 89.141 3342 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 30.83 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.52 % Favored : 93.97 % Rotamer: Outliers : 4.69 % Allowed : 3.34 % Favored : 91.97 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.26), residues: 1160 helix: 1.12 (0.27), residues: 429 sheet: -0.78 (0.35), residues: 232 loop : -1.33 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 36 HIS 0.005 0.001 HIS R 44 PHE 0.024 0.001 PHE B 253 TYR 0.015 0.001 TYR N 115 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 THR cc_start: 0.5987 (t) cc_final: 0.5655 (t) REVERT: A 278 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: B 17 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8795 (pp30) REVERT: B 188 MET cc_start: 0.8680 (mmm) cc_final: 0.8290 (mmm) REVERT: B 254 ASP cc_start: 0.8054 (t70) cc_final: 0.7834 (t0) REVERT: C 13 ARG cc_start: 0.9337 (ttm110) cc_final: 0.9136 (ttm110) REVERT: C 42 GLU cc_start: 0.8809 (pp20) cc_final: 0.8443 (pp20) REVERT: N 2 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8200 (p) REVERT: R 34 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8753 (tm-30) REVERT: R 142 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8161 (mt0) REVERT: R 354 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8546 (tt) REVERT: R 362 GLU cc_start: 0.8769 (tp30) cc_final: 0.8552 (tp30) REVERT: R 407 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8825 (p) outliers start: 45 outliers final: 7 residues processed: 217 average time/residue: 1.2928 time to fit residues: 298.2455 Evaluate side-chains 139 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 142 GLN Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS A 197 GLN B 340 ASN C 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 142 GLN R 177 HIS R 179 ASN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 337 GLN ** R 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 408 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.100863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.071116 restraints weight = 19163.498| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.40 r_work: 0.2936 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9397 Z= 0.245 Angle : 0.656 9.862 12743 Z= 0.339 Chirality : 0.043 0.226 1414 Planarity : 0.005 0.068 1634 Dihedral : 6.722 74.355 1324 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.22 % Favored : 95.60 % Rotamer: Outliers : 2.29 % Allowed : 14.60 % Favored : 83.11 % 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: -0.09 (0.25), residues: 1160 helix: 1.51 (0.26), residues: 438 sheet: -0.60 (0.35), residues: 232 loop : -1.22 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 36 HIS 0.008 0.001 HIS R 361 PHE 0.023 0.002 PHE P 6 TYR 0.027 0.002 TYR R 145 ARG 0.006 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 4.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8750 (mm-30) REVERT: B 8 ARG cc_start: 0.9410 (mtp180) cc_final: 0.8787 (mtt180) REVERT: B 15 LYS cc_start: 0.9344 (tttt) cc_final: 0.8955 (tmmt) REVERT: B 32 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7219 (pm20) REVERT: B 188 MET cc_start: 0.9172 (mmm) cc_final: 0.8764 (mmm) REVERT: B 254 ASP cc_start: 0.8253 (t70) cc_final: 0.7910 (t0) REVERT: B 260 GLU cc_start: 0.8360 (pt0) cc_final: 0.7743 (tt0) REVERT: B 262 MET cc_start: 0.8719 (tpt) cc_final: 0.8257 (tpp) REVERT: B 298 ASP cc_start: 0.8758 (t0) cc_final: 0.8371 (t0) REVERT: B 301 LYS cc_start: 0.7793 (mmpt) cc_final: 0.7452 (mmmt) REVERT: C 13 ARG cc_start: 0.9346 (ttm110) cc_final: 0.9131 (ttm110) REVERT: C 29 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8493 (mmmm) REVERT: C 42 GLU cc_start: 0.8825 (pp20) cc_final: 0.8465 (pp20) REVERT: C 58 GLU cc_start: 0.9367 (mm-30) cc_final: 0.8825 (mt-10) REVERT: N 87 LYS cc_start: 0.8604 (tppp) cc_final: 0.8226 (ttmp) REVERT: N 89 GLU cc_start: 0.8791 (pm20) cc_final: 0.8533 (pm20) REVERT: N 94 TYR cc_start: 0.9036 (m-80) cc_final: 0.8727 (m-80) REVERT: R 34 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8971 (tm-30) REVERT: R 349 LYS cc_start: 0.6217 (mmtt) cc_final: 0.5967 (mptt) REVERT: R 354 LEU cc_start: 0.9054 (tp) cc_final: 0.8771 (tp) REVERT: R 410 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8550 (tm-30) outliers start: 22 outliers final: 14 residues processed: 167 average time/residue: 1.8051 time to fit residues: 324.8846 Evaluate side-chains 158 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 133 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 77 optimal weight: 0.0270 chunk 109 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN ** R 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.101925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.071433 restraints weight = 19586.376| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.44 r_work: 0.2879 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9397 Z= 0.245 Angle : 0.611 9.251 12743 Z= 0.318 Chirality : 0.042 0.156 1414 Planarity : 0.004 0.071 1634 Dihedral : 5.507 59.539 1304 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.40 % Favored : 95.43 % Rotamer: Outliers : 3.13 % Allowed : 16.89 % Favored : 79.98 % 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: 0.17 (0.26), residues: 1160 helix: 1.80 (0.26), residues: 427 sheet: -0.48 (0.34), residues: 234 loop : -1.08 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 36 HIS 0.010 0.001 HIS R 361 PHE 0.019 0.001 PHE P 6 TYR 0.025 0.002 TYR R 145 ARG 0.005 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8838 (mm-30) REVERT: A 246 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: B 8 ARG cc_start: 0.9323 (mtp180) cc_final: 0.8936 (mtt180) REVERT: B 15 LYS cc_start: 0.9385 (tttt) cc_final: 0.9012 (tmmt) REVERT: B 17 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8666 (pp30) REVERT: B 32 GLN cc_start: 0.7620 (pm20) cc_final: 0.7304 (pm20) REVERT: B 158 VAL cc_start: 0.9294 (t) cc_final: 0.8969 (p) REVERT: B 188 MET cc_start: 0.9178 (mmm) cc_final: 0.8700 (mmm) REVERT: B 260 GLU cc_start: 0.8455 (pt0) cc_final: 0.8057 (tt0) REVERT: B 262 MET cc_start: 0.8763 (tpt) cc_final: 0.8322 (tpp) REVERT: C 13 ARG cc_start: 0.9326 (ttm110) cc_final: 0.9112 (ttm110) REVERT: C 20 LYS cc_start: 0.8890 (tmmt) cc_final: 0.8602 (tmmt) REVERT: C 29 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8529 (tppp) REVERT: C 42 GLU cc_start: 0.8855 (pp20) cc_final: 0.8456 (pp20) REVERT: C 58 GLU cc_start: 0.9416 (mm-30) cc_final: 0.8858 (mt-10) REVERT: N 87 LYS cc_start: 0.8522 (tppp) cc_final: 0.8078 (ttmp) REVERT: N 89 GLU cc_start: 0.8825 (pm20) cc_final: 0.8617 (pm20) REVERT: R 34 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8978 (tm-30) REVERT: R 115 TRP cc_start: 0.8723 (m100) cc_final: 0.8448 (m100) REVERT: R 133 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8663 (mp0) REVERT: R 290 GLU cc_start: 0.6731 (pp20) cc_final: 0.6383 (pp20) REVERT: R 354 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8851 (tp) outliers start: 30 outliers final: 16 residues processed: 163 average time/residue: 1.2728 time to fit residues: 222.2685 Evaluate side-chains 148 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN ** R 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.072958 restraints weight = 19317.824| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.38 r_work: 0.2916 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9397 Z= 0.198 Angle : 0.598 10.096 12743 Z= 0.308 Chirality : 0.041 0.162 1414 Planarity : 0.004 0.073 1634 Dihedral : 5.288 57.473 1304 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.88 % Favored : 95.95 % Rotamer: Outliers : 2.92 % Allowed : 19.40 % Favored : 77.69 % 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 (0.26), residues: 1160 helix: 1.79 (0.26), residues: 433 sheet: -0.36 (0.34), residues: 239 loop : -0.98 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP N 36 HIS 0.009 0.001 HIS R 361 PHE 0.017 0.001 PHE P 6 TYR 0.023 0.001 TYR R 145 ARG 0.007 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8820 (mm-30) REVERT: B 15 LYS cc_start: 0.9389 (tttt) cc_final: 0.9038 (tmmt) REVERT: B 32 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7394 (pm20) REVERT: B 158 VAL cc_start: 0.9313 (t) cc_final: 0.9022 (p) REVERT: B 188 MET cc_start: 0.9187 (mmm) cc_final: 0.8743 (mmm) REVERT: B 217 MET cc_start: 0.7491 (pmm) cc_final: 0.7051 (pmm) REVERT: B 254 ASP cc_start: 0.8187 (t70) cc_final: 0.7843 (t0) REVERT: B 260 GLU cc_start: 0.8394 (pt0) cc_final: 0.7963 (tt0) REVERT: B 262 MET cc_start: 0.8729 (tpt) cc_final: 0.8305 (tpp) REVERT: B 298 ASP cc_start: 0.8653 (t0) cc_final: 0.8353 (t0) REVERT: C 13 ARG cc_start: 0.9334 (ttm110) cc_final: 0.9117 (ttm110) REVERT: C 42 GLU cc_start: 0.8835 (pp20) cc_final: 0.8440 (pp20) REVERT: C 58 GLU cc_start: 0.9438 (mm-30) cc_final: 0.8912 (mt-10) REVERT: N 38 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8960 (ptm-80) REVERT: N 82 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8061 (tp-100) REVERT: N 87 LYS cc_start: 0.8541 (tppp) cc_final: 0.8198 (ttmm) REVERT: N 89 GLU cc_start: 0.8900 (pm20) cc_final: 0.8687 (pm20) REVERT: R 34 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8978 (tm-30) REVERT: R 50 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8182 (tp) REVERT: R 115 TRP cc_start: 0.8727 (m100) cc_final: 0.8475 (m100) REVERT: R 166 LEU cc_start: 0.8072 (tp) cc_final: 0.7828 (tp) REVERT: R 354 LEU cc_start: 0.9130 (tp) cc_final: 0.8922 (tp) outliers start: 28 outliers final: 15 residues processed: 166 average time/residue: 1.1591 time to fit residues: 206.0715 Evaluate side-chains 151 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 235 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN ** R 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.096815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.066350 restraints weight = 19581.610| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.43 r_work: 0.2829 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9397 Z= 0.323 Angle : 0.636 9.132 12743 Z= 0.330 Chirality : 0.043 0.158 1414 Planarity : 0.004 0.078 1634 Dihedral : 5.502 55.452 1304 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.40 % Favored : 95.43 % Rotamer: Outliers : 3.86 % Allowed : 20.54 % Favored : 75.60 % 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: 0.33 (0.26), residues: 1160 helix: 1.86 (0.25), residues: 431 sheet: -0.40 (0.34), residues: 243 loop : -0.93 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP N 36 HIS 0.010 0.001 HIS R 361 PHE 0.017 0.002 PHE P 6 TYR 0.024 0.002 TYR R 145 ARG 0.009 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8782 (mm-30) REVERT: B 8 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.8993 (mtm110) REVERT: B 15 LYS cc_start: 0.9406 (tttt) cc_final: 0.9115 (tmmt) REVERT: B 188 MET cc_start: 0.9152 (mmm) cc_final: 0.8774 (mmm) REVERT: B 217 MET cc_start: 0.7608 (pmm) cc_final: 0.7228 (pmm) REVERT: B 254 ASP cc_start: 0.8203 (t70) cc_final: 0.7837 (t0) REVERT: B 260 GLU cc_start: 0.8533 (pt0) cc_final: 0.8017 (tt0) REVERT: B 262 MET cc_start: 0.8730 (tpt) cc_final: 0.8224 (tpp) REVERT: C 13 ARG cc_start: 0.9367 (ttm110) cc_final: 0.9140 (ttm110) REVERT: C 42 GLU cc_start: 0.8913 (pp20) cc_final: 0.8479 (pp20) REVERT: C 58 GLU cc_start: 0.9408 (mm-30) cc_final: 0.8843 (mt-10) REVERT: N 38 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8606 (ptm160) REVERT: N 46 GLU cc_start: 0.8472 (pt0) cc_final: 0.8269 (pt0) REVERT: N 87 LYS cc_start: 0.8540 (tppp) cc_final: 0.8141 (ttmm) REVERT: R 34 GLU cc_start: 0.9278 (tm-30) cc_final: 0.9007 (tm-30) REVERT: R 115 TRP cc_start: 0.8682 (m100) cc_final: 0.8460 (m100) REVERT: R 127 GLU cc_start: 0.7700 (mp0) cc_final: 0.7153 (mp0) REVERT: R 354 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8901 (tp) outliers start: 37 outliers final: 20 residues processed: 155 average time/residue: 1.2857 time to fit residues: 213.2613 Evaluate side-chains 154 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 104 optimal weight: 0.6980 chunk 37 optimal weight: 0.0050 chunk 95 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN C 24 ASN ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.099116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.069407 restraints weight = 19092.125| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.36 r_work: 0.2893 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9397 Z= 0.186 Angle : 0.612 10.256 12743 Z= 0.311 Chirality : 0.041 0.161 1414 Planarity : 0.004 0.078 1634 Dihedral : 5.215 54.151 1302 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.57 % Favored : 95.34 % Rotamer: Outliers : 3.55 % Allowed : 21.38 % Favored : 75.08 % 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: 0.46 (0.26), residues: 1160 helix: 1.86 (0.26), residues: 443 sheet: -0.29 (0.34), residues: 238 loop : -0.83 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 36 HIS 0.009 0.001 HIS R 361 PHE 0.016 0.001 PHE P 6 TYR 0.022 0.001 TYR R 145 ARG 0.011 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8739 (mm-30) REVERT: B 8 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.8852 (ptp90) REVERT: B 15 LYS cc_start: 0.9346 (tttt) cc_final: 0.9096 (tmmt) REVERT: B 32 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: B 158 VAL cc_start: 0.9302 (t) cc_final: 0.9014 (p) REVERT: B 188 MET cc_start: 0.9165 (mmm) cc_final: 0.8707 (mmm) REVERT: B 217 MET cc_start: 0.7675 (pmm) cc_final: 0.7258 (pmm) REVERT: B 254 ASP cc_start: 0.8187 (t70) cc_final: 0.7796 (t0) REVERT: B 260 GLU cc_start: 0.8351 (pt0) cc_final: 0.7933 (tt0) REVERT: B 262 MET cc_start: 0.8695 (tpt) cc_final: 0.8218 (tpp) REVERT: C 13 ARG cc_start: 0.9347 (ttm110) cc_final: 0.9122 (ttm110) REVERT: C 42 GLU cc_start: 0.8829 (pp20) cc_final: 0.8409 (pp20) REVERT: C 58 GLU cc_start: 0.9418 (mm-30) cc_final: 0.8894 (mt-10) REVERT: N 38 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8567 (ptm160) REVERT: N 46 GLU cc_start: 0.8380 (pt0) cc_final: 0.8178 (pt0) REVERT: N 87 LYS cc_start: 0.8548 (tppp) cc_final: 0.8306 (ttmm) REVERT: N 89 GLU cc_start: 0.8794 (pm20) cc_final: 0.8539 (pm20) REVERT: R 34 GLU cc_start: 0.9271 (tm-30) cc_final: 0.9002 (tm-30) REVERT: R 115 TRP cc_start: 0.8709 (m100) cc_final: 0.8479 (m100) REVERT: R 127 GLU cc_start: 0.7743 (mp0) cc_final: 0.7222 (mp0) REVERT: R 290 GLU cc_start: 0.6943 (pp20) cc_final: 0.6656 (pp20) outliers start: 34 outliers final: 21 residues processed: 160 average time/residue: 1.5184 time to fit residues: 261.0995 Evaluate side-chains 155 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.7045 > 50: distance: 25 - 135: 30.209 distance: 44 - 67: 37.620 distance: 54 - 72: 24.944 distance: 59 - 78: 31.640 distance: 62 - 67: 34.692 distance: 63 - 86: 31.567 distance: 67 - 68: 40.288 distance: 68 - 69: 20.208 distance: 68 - 71: 16.662 distance: 69 - 70: 26.591 distance: 69 - 72: 47.327 distance: 72 - 73: 15.010 distance: 73 - 74: 33.188 distance: 73 - 76: 58.956 distance: 74 - 75: 12.444 distance: 74 - 78: 48.915 distance: 76 - 77: 51.603 distance: 78 - 79: 21.269 distance: 79 - 80: 39.103 distance: 79 - 82: 16.696 distance: 80 - 81: 40.530 distance: 80 - 86: 58.988 distance: 82 - 83: 51.263 distance: 83 - 84: 12.550 distance: 83 - 85: 32.803 distance: 86 - 87: 55.510 distance: 87 - 88: 41.206 distance: 87 - 90: 45.520 distance: 88 - 89: 47.080 distance: 88 - 97: 44.195 distance: 90 - 91: 36.718 distance: 91 - 92: 41.952 distance: 91 - 93: 45.028 distance: 92 - 94: 41.827 distance: 93 - 95: 40.772 distance: 94 - 96: 21.376 distance: 95 - 96: 21.940 distance: 97 - 98: 10.219 distance: 98 - 99: 35.841 distance: 98 - 101: 45.716 distance: 99 - 100: 42.885 distance: 99 - 106: 41.635 distance: 101 - 102: 47.886 distance: 102 - 103: 30.630 distance: 103 - 104: 15.476 distance: 103 - 105: 14.983 distance: 106 - 107: 39.719 distance: 107 - 108: 35.803 distance: 107 - 110: 42.381 distance: 108 - 109: 34.296 distance: 108 - 114: 51.151 distance: 110 - 111: 40.674 distance: 111 - 112: 50.154 distance: 111 - 113: 57.492 distance: 114 - 115: 10.453 distance: 115 - 116: 15.887 distance: 115 - 118: 33.530 distance: 116 - 117: 36.964 distance: 116 - 121: 40.600 distance: 118 - 119: 27.606 distance: 118 - 120: 33.049 distance: 121 - 122: 39.621 distance: 122 - 123: 35.433 distance: 122 - 125: 28.565 distance: 123 - 124: 27.266 distance: 123 - 130: 23.091 distance: 125 - 126: 34.414 distance: 126 - 127: 8.340 distance: 127 - 128: 13.951 distance: 127 - 129: 30.026 distance: 130 - 131: 10.040 distance: 131 - 132: 30.401 distance: 131 - 134: 31.904 distance: 132 - 133: 43.977 distance: 132 - 136: 55.390 distance: 134 - 135: 44.882 distance: 136 - 137: 52.712 distance: 137 - 138: 44.419 distance: 137 - 140: 56.792 distance: 138 - 139: 42.512 distance: 138 - 150: 28.460 distance: 140 - 141: 45.490 distance: 141 - 142: 16.592 distance: 141 - 143: 12.043 distance: 142 - 144: 28.490 distance: 143 - 145: 21.277 distance: 143 - 146: 14.035 distance: 144 - 145: 9.722 distance: 145 - 147: 6.986 distance: 146 - 148: 7.996 distance: 147 - 149: 7.879 distance: 148 - 149: 6.783