Starting phenix.real_space_refine on Fri Aug 22 20:57:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cx2_30489/08_2025/7cx2_30489.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cx2_30489/08_2025/7cx2_30489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cx2_30489/08_2025/7cx2_30489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cx2_30489/08_2025/7cx2_30489.map" model { file = "/net/cci-nas-00/data/ceres_data/7cx2_30489/08_2025/7cx2_30489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cx2_30489/08_2025/7cx2_30489.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.009 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 52 5.16 5 C 5027 2.51 5 N 1374 2.21 5 O 1477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7930 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2027 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1870 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2598 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 1.67, per 1000 atoms: 0.21 Number of scatterers: 7930 At special positions: 0 Unit cell: (77.064, 110.526, 125.736, 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 52 16.00 O 1477 8.00 N 1374 7.00 C 5027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 295.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 40.8% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'R' and resid 26 through 46 removed outlier: 3.910A pdb=" N VAL R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY R 35 " --> pdb=" O MET R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 83 removed outlier: 3.859A pdb=" N GLU R 73 " --> pdb=" O VAL R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 94 removed outlier: 3.933A pdb=" N TYR R 93 " --> pdb=" O VAL R 89 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 140 Processing helix chain 'R' and resid 140 through 148 removed outlier: 3.685A pdb=" N VAL R 148 " --> pdb=" O TYR R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 154 removed outlier: 3.793A pdb=" N LEU R 154 " --> pdb=" O SER R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 170 Processing helix chain 'R' and resid 171 through 174 Processing helix chain 'R' and resid 195 through 228 Processing helix chain 'R' and resid 258 through 277 removed outlier: 3.661A pdb=" N SER R 277 " --> pdb=" O PHE R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 284 removed outlier: 4.037A pdb=" N THR R 281 " --> pdb=" O SER R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 317 removed outlier: 3.821A pdb=" N LEU R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER R 305 " --> pdb=" O LEU R 301 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN R 307 " --> pdb=" O PHE R 303 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 319 through 330 Processing helix chain 'A' and resid 13 through 38 removed outlier: 3.663A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 4.296A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.549A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.339A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.902A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.899A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.001A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.681A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 4.056A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.982A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.591A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.675A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 180 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.733A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.630A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.873A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.929A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.590A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.997A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.623A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.874A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.822A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1293 1.31 - 1.44: 2222 1.44 - 1.57: 4495 1.57 - 1.70: 2 1.70 - 1.83: 74 Bond restraints: 8086 Sorted by residual: bond pdb=" C8 P2E R 401 " pdb=" C9 P2E R 401 " ideal model delta sigma weight residual 1.515 1.436 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C11 P2E R 401 " pdb=" O4 P2E R 401 " ideal model delta sigma weight residual 1.402 1.330 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C10 P2E R 401 " pdb=" C11 P2E R 401 " ideal model delta sigma weight residual 1.529 1.598 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C7 P2E R 401 " pdb=" C8 P2E R 401 " ideal model delta sigma weight residual 1.529 1.576 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" C12 P2E R 401 " pdb=" C8 P2E R 401 " ideal model delta sigma weight residual 1.538 1.498 0.040 2.00e-02 2.50e+03 4.07e+00 ... (remaining 8081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 10881 2.97 - 5.95: 70 5.95 - 8.92: 7 8.92 - 11.89: 1 11.89 - 14.87: 4 Bond angle restraints: 10963 Sorted by residual: angle pdb=" N VAL R 156 " pdb=" CA VAL R 156 " pdb=" C VAL R 156 " ideal model delta sigma weight residual 110.62 116.74 -6.12 1.02e+00 9.61e-01 3.59e+01 angle pdb=" N ASP A 354 " pdb=" CA ASP A 354 " pdb=" C ASP A 354 " ideal model delta sigma weight residual 111.28 116.79 -5.51 1.09e+00 8.42e-01 2.56e+01 angle pdb=" C4 P2E R 401 " pdb=" C5 P2E R 401 " pdb=" C6 P2E R 401 " ideal model delta sigma weight residual 127.52 112.65 14.87 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C5 P2E R 401 " pdb=" C6 P2E R 401 " pdb=" C7 P2E R 401 " ideal model delta sigma weight residual 125.83 111.98 13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" N GLN A 390 " pdb=" CA GLN A 390 " pdb=" C GLN A 390 " ideal model delta sigma weight residual 111.71 116.83 -5.12 1.15e+00 7.56e-01 1.98e+01 ... (remaining 10958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 4337 16.25 - 32.49: 395 32.49 - 48.74: 83 48.74 - 64.98: 17 64.98 - 81.23: 9 Dihedral angle restraints: 4841 sinusoidal: 1870 harmonic: 2971 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 -4.97 -81.03 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 4838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1024 0.059 - 0.119: 206 0.119 - 0.178: 19 0.178 - 0.238: 1 0.238 - 0.297: 2 Chirality restraints: 1252 Sorted by residual: chirality pdb=" C15 P2E R 401 " pdb=" C14 P2E R 401 " pdb=" C16 P2E R 401 " pdb=" O5 P2E R 401 " both_signs ideal model delta sigma weight residual False 2.23 2.52 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C8 P2E R 401 " pdb=" C12 P2E R 401 " pdb=" C7 P2E R 401 " pdb=" C9 P2E R 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.78 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA GLN A 390 " pdb=" N GLN A 390 " pdb=" C GLN A 390 " pdb=" CB GLN A 390 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1249 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 P2E R 401 " -0.269 2.00e-02 2.50e+03 2.73e-01 7.46e+02 pdb=" C13 P2E R 401 " 0.249 2.00e-02 2.50e+03 pdb=" C14 P2E R 401 " 0.296 2.00e-02 2.50e+03 pdb=" C15 P2E R 401 " -0.277 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 388 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C LEU A 388 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU A 388 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG A 389 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 P2E R 401 " -0.028 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C5 P2E R 401 " 0.028 2.00e-02 2.50e+03 pdb=" C6 P2E R 401 " 0.028 2.00e-02 2.50e+03 pdb=" C7 P2E R 401 " -0.028 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 93 2.65 - 3.21: 7115 3.21 - 3.78: 11836 3.78 - 4.34: 17133 4.34 - 4.90: 28054 Nonbonded interactions: 64231 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.088 3.040 nonbonded pdb=" OG1 THR R 82 " pdb=" O HOH R 501 " model vdw 2.133 3.040 nonbonded pdb=" O SER N 52 " pdb=" NH1 ARG N 72 " model vdw 2.247 3.120 nonbonded pdb=" O GLU A 50 " pdb=" NH2 ARG A 265 " model vdw 2.276 3.120 nonbonded pdb=" O LEU R 304 " pdb=" ND2 ASN R 307 " model vdw 2.280 3.120 ... (remaining 64226 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.900 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.004 0.079 8089 Z= 0.206 Angle : 0.713 14.865 10969 Z= 0.397 Chirality : 0.047 0.297 1252 Planarity : 0.009 0.273 1402 Dihedral : 13.642 81.229 2908 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.12 % Allowed : 4.17 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.23), residues: 1002 helix: -0.55 (0.24), residues: 371 sheet: -0.79 (0.32), residues: 210 loop : -2.51 (0.24), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 228 TYR 0.024 0.002 TYR B 59 PHE 0.015 0.002 PHE A 212 TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8086) covalent geometry : angle 0.71159 (10963) SS BOND : bond 0.00171 ( 3) SS BOND : angle 1.93365 ( 6) hydrogen bonds : bond 0.14524 ( 394) hydrogen bonds : angle 5.49290 ( 1125) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7395 (t80) cc_final: 0.6912 (t80) REVERT: R 116 MET cc_start: 0.7244 (tpp) cc_final: 0.6897 (tpp) REVERT: R 124 MET cc_start: 0.8306 (tpp) cc_final: 0.8033 (tpt) REVERT: R 126 MET cc_start: 0.8307 (tpt) cc_final: 0.8107 (tpt) REVERT: R 282 ILE cc_start: 0.8561 (tt) cc_final: 0.8311 (pt) REVERT: A 20 ARG cc_start: 0.7012 (mtp85) cc_final: 0.6757 (tpp80) REVERT: A 24 LYS cc_start: 0.7859 (ttpp) cc_final: 0.7567 (ttmm) REVERT: B 23 LYS cc_start: 0.8989 (tttp) cc_final: 0.8746 (ttpp) REVERT: B 32 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8284 (tp-100) REVERT: N 12 VAL cc_start: 0.9235 (p) cc_final: 0.9015 (m) REVERT: N 105 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7787 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.6218 time to fit residues: 112.1852 Evaluate side-chains 124 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 213 GLN A 390 GLN B 17 GLN B 175 GLN B 176 GLN N 35 ASN N 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.156159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105758 restraints weight = 9786.272| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.62 r_work: 0.3146 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8089 Z= 0.122 Angle : 0.545 7.700 10969 Z= 0.281 Chirality : 0.042 0.140 1252 Planarity : 0.004 0.054 1402 Dihedral : 5.531 55.062 1140 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.15 % Allowed : 12.75 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.25), residues: 1002 helix: 1.06 (0.27), residues: 382 sheet: -0.39 (0.33), residues: 211 loop : -2.03 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 72 TYR 0.010 0.001 TYR B 124 PHE 0.019 0.001 PHE R 119 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8086) covalent geometry : angle 0.54458 (10963) SS BOND : bond 0.00103 ( 3) SS BOND : angle 1.43327 ( 6) hydrogen bonds : bond 0.03785 ( 394) hydrogen bonds : angle 4.15347 ( 1125) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: R 116 MET cc_start: 0.6896 (tpp) cc_final: 0.6615 (tpp) REVERT: R 228 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6707 (mtp85) REVERT: R 282 ILE cc_start: 0.8428 (tt) cc_final: 0.8107 (pt) REVERT: A 20 ARG cc_start: 0.7063 (mtp85) cc_final: 0.6813 (tpp80) REVERT: A 24 LYS cc_start: 0.7702 (ttpp) cc_final: 0.7123 (ttmm) REVERT: A 318 TYR cc_start: 0.7077 (t80) cc_final: 0.6645 (t80) REVERT: B 23 LYS cc_start: 0.8531 (tttp) cc_final: 0.8209 (ttpp) REVERT: B 32 GLN cc_start: 0.8765 (tp-100) cc_final: 0.8542 (tp-100) REVERT: B 160 SER cc_start: 0.8899 (m) cc_final: 0.8444 (p) REVERT: B 170 ASP cc_start: 0.8033 (t0) cc_final: 0.7769 (t0) REVERT: B 175 GLN cc_start: 0.8774 (mt0) cc_final: 0.8535 (pt0) REVERT: B 217 MET cc_start: 0.8304 (ptm) cc_final: 0.7781 (pp-130) REVERT: B 259 GLN cc_start: 0.8167 (pt0) cc_final: 0.7926 (pt0) REVERT: N 73 ASP cc_start: 0.7011 (t70) cc_final: 0.6057 (p0) REVERT: N 78 THR cc_start: 0.8750 (m) cc_final: 0.8292 (m) REVERT: N 105 ARG cc_start: 0.8302 (mtp180) cc_final: 0.7717 (mtm-85) outliers start: 18 outliers final: 7 residues processed: 151 average time/residue: 0.6153 time to fit residues: 97.5802 Evaluate side-chains 139 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 ASN A 23 ASN A 29 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.151575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101320 restraints weight = 9725.171| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.59 r_work: 0.3071 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8089 Z= 0.234 Angle : 0.608 8.647 10969 Z= 0.315 Chirality : 0.045 0.157 1252 Planarity : 0.005 0.057 1402 Dihedral : 5.810 58.066 1140 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.74 % Allowed : 16.45 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.26), residues: 1002 helix: 1.52 (0.27), residues: 382 sheet: -0.32 (0.34), residues: 213 loop : -1.78 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 228 TYR 0.020 0.002 TYR B 105 PHE 0.018 0.002 PHE A 212 TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 8086) covalent geometry : angle 0.60649 (10963) SS BOND : bond 0.00230 ( 3) SS BOND : angle 2.07924 ( 6) hydrogen bonds : bond 0.04351 ( 394) hydrogen bonds : angle 4.22282 ( 1125) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7154 (t80) cc_final: 0.6754 (t80) REVERT: R 282 ILE cc_start: 0.8438 (tt) cc_final: 0.8111 (pt) REVERT: A 20 ARG cc_start: 0.7237 (mtp85) cc_final: 0.6984 (tpp80) REVERT: A 24 LYS cc_start: 0.7791 (ttpp) cc_final: 0.7277 (ttmm) REVERT: A 220 HIS cc_start: 0.8167 (m170) cc_final: 0.7836 (m-70) REVERT: A 314 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7963 (tm-30) REVERT: B 19 ARG cc_start: 0.7240 (ttm110) cc_final: 0.6906 (ttm110) REVERT: B 23 LYS cc_start: 0.8656 (tttp) cc_final: 0.8253 (ttpp) REVERT: B 32 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8601 (tp-100) REVERT: B 111 TYR cc_start: 0.9077 (m-80) cc_final: 0.8770 (m-80) REVERT: B 175 GLN cc_start: 0.8736 (mt0) cc_final: 0.8524 (pt0) REVERT: B 214 ARG cc_start: 0.7732 (mpt180) cc_final: 0.7393 (mpt180) REVERT: B 217 MET cc_start: 0.8396 (ptm) cc_final: 0.8183 (pp-130) REVERT: B 271 CYS cc_start: 0.8905 (p) cc_final: 0.8439 (p) REVERT: G 17 GLU cc_start: 0.8241 (tp30) cc_final: 0.8041 (tp30) REVERT: N 73 ASP cc_start: 0.7162 (t70) cc_final: 0.6708 (t70) REVERT: N 89 GLU cc_start: 0.9114 (mp0) cc_final: 0.8914 (mp0) REVERT: N 105 ARG cc_start: 0.8355 (mtp180) cc_final: 0.7755 (mtm-85) outliers start: 23 outliers final: 11 residues processed: 149 average time/residue: 0.5866 time to fit residues: 91.6759 Evaluate side-chains 136 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN B 13 GLN B 266 HIS N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.154867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104302 restraints weight = 9890.317| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.63 r_work: 0.3134 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8089 Z= 0.116 Angle : 0.530 10.463 10969 Z= 0.269 Chirality : 0.041 0.141 1252 Planarity : 0.004 0.057 1402 Dihedral : 5.590 58.236 1140 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.38 % Allowed : 17.88 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.27), residues: 1002 helix: 1.82 (0.28), residues: 382 sheet: -0.11 (0.34), residues: 212 loop : -1.51 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 19 TYR 0.010 0.001 TYR B 124 PHE 0.029 0.001 PHE R 119 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8086) covalent geometry : angle 0.52904 (10963) SS BOND : bond 0.00165 ( 3) SS BOND : angle 1.33202 ( 6) hydrogen bonds : bond 0.03416 ( 394) hydrogen bonds : angle 3.90897 ( 1125) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7012 (t80) cc_final: 0.6644 (t80) REVERT: R 116 MET cc_start: 0.7194 (tpp) cc_final: 0.6760 (tpt) REVERT: R 228 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6714 (mtp85) REVERT: R 282 ILE cc_start: 0.8428 (tt) cc_final: 0.8107 (pt) REVERT: A 20 ARG cc_start: 0.7071 (mtp85) cc_final: 0.6821 (tpp80) REVERT: A 24 LYS cc_start: 0.7654 (ttpp) cc_final: 0.7138 (ttmm) REVERT: A 314 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 356 ARG cc_start: 0.8379 (pmm-80) cc_final: 0.8019 (ptp-170) REVERT: B 19 ARG cc_start: 0.7220 (ttm110) cc_final: 0.6950 (ttm110) REVERT: B 23 LYS cc_start: 0.8618 (tttp) cc_final: 0.8224 (ttpp) REVERT: B 32 GLN cc_start: 0.8808 (tp-100) cc_final: 0.8408 (tp-100) REVERT: B 46 ARG cc_start: 0.8378 (ptp-110) cc_final: 0.7625 (mtt90) REVERT: B 170 ASP cc_start: 0.8023 (t0) cc_final: 0.7736 (t0) REVERT: B 214 ARG cc_start: 0.7737 (mpt180) cc_final: 0.7334 (mpt180) REVERT: B 217 MET cc_start: 0.8394 (ptm) cc_final: 0.8185 (pp-130) REVERT: B 271 CYS cc_start: 0.8753 (p) cc_final: 0.8217 (p) REVERT: G 17 GLU cc_start: 0.8308 (tp30) cc_final: 0.8080 (tp30) REVERT: N 89 GLU cc_start: 0.9102 (mp0) cc_final: 0.8888 (mp0) REVERT: N 105 ARG cc_start: 0.8319 (mtp180) cc_final: 0.7711 (mtm-85) outliers start: 20 outliers final: 11 residues processed: 145 average time/residue: 0.6153 time to fit residues: 93.7413 Evaluate side-chains 139 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 ASN B 13 GLN G 5 ASN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.153314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.102712 restraints weight = 9900.063| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.61 r_work: 0.3106 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8089 Z= 0.158 Angle : 0.555 8.764 10969 Z= 0.284 Chirality : 0.042 0.145 1252 Planarity : 0.004 0.056 1402 Dihedral : 5.472 55.265 1140 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.22 % Allowed : 19.07 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.27), residues: 1002 helix: 1.98 (0.28), residues: 382 sheet: -0.05 (0.33), residues: 218 loop : -1.38 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 19 TYR 0.013 0.001 TYR B 105 PHE 0.036 0.002 PHE R 119 TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8086) covalent geometry : angle 0.55378 (10963) SS BOND : bond 0.00201 ( 3) SS BOND : angle 1.67435 ( 6) hydrogen bonds : bond 0.03615 ( 394) hydrogen bonds : angle 3.94128 ( 1125) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: R 116 MET cc_start: 0.7153 (tpp) cc_final: 0.6517 (tpt) REVERT: R 228 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6788 (mtp85) REVERT: R 282 ILE cc_start: 0.8398 (tt) cc_final: 0.8131 (pt) REVERT: A 20 ARG cc_start: 0.7095 (mtp85) cc_final: 0.6850 (tpp80) REVERT: A 24 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7158 (ttmm) REVERT: A 220 HIS cc_start: 0.8007 (m-70) cc_final: 0.7773 (m-70) REVERT: A 314 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7815 (tm-30) REVERT: A 356 ARG cc_start: 0.8477 (pmm-80) cc_final: 0.7987 (pmm-80) REVERT: B 19 ARG cc_start: 0.7224 (ttm110) cc_final: 0.6939 (ttm110) REVERT: B 23 LYS cc_start: 0.8588 (tttp) cc_final: 0.8170 (ttpp) REVERT: B 32 GLN cc_start: 0.8749 (tp-100) cc_final: 0.8438 (tp-100) REVERT: B 46 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7566 (mtt90) REVERT: B 111 TYR cc_start: 0.8987 (m-80) cc_final: 0.8733 (m-80) REVERT: B 170 ASP cc_start: 0.8028 (t0) cc_final: 0.7756 (t0) REVERT: B 214 ARG cc_start: 0.7787 (mpt180) cc_final: 0.7397 (mpt180) REVERT: B 217 MET cc_start: 0.8412 (ptm) cc_final: 0.8152 (pp-130) REVERT: B 262 MET cc_start: 0.9291 (mmt) cc_final: 0.9067 (mmt) REVERT: B 271 CYS cc_start: 0.8801 (p) cc_final: 0.8279 (p) REVERT: G 17 GLU cc_start: 0.8419 (tp30) cc_final: 0.8190 (tp30) REVERT: N 89 GLU cc_start: 0.9101 (mp0) cc_final: 0.8885 (mp0) REVERT: N 105 ARG cc_start: 0.8293 (mtp180) cc_final: 0.7680 (mtm-85) outliers start: 27 outliers final: 15 residues processed: 137 average time/residue: 0.6123 time to fit residues: 88.1458 Evaluate side-chains 135 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 5 ASN Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.5018 > 50: distance: 53 - 126: 12.779 distance: 56 - 123: 5.830 distance: 65 - 114: 9.174 distance: 68 - 111: 5.097 distance: 91 - 95: 6.458 distance: 95 - 96: 5.529 distance: 96 - 97: 10.530 distance: 96 - 99: 12.759 distance: 97 - 98: 8.442 distance: 100 - 101: 4.081 distance: 100 - 188: 7.992 distance: 101 - 102: 4.311 distance: 101 - 104: 8.533 distance: 102 - 111: 11.259 distance: 103 - 185: 4.216 distance: 104 - 105: 4.524 distance: 105 - 106: 9.568 distance: 105 - 107: 12.818 distance: 106 - 108: 8.625 distance: 107 - 109: 11.903 distance: 108 - 110: 6.480 distance: 109 - 110: 13.460 distance: 111 - 112: 6.739 distance: 112 - 113: 7.729 distance: 112 - 115: 18.657 distance: 113 - 114: 7.602 distance: 113 - 116: 8.796 distance: 117 - 118: 14.257 distance: 117 - 120: 3.952 distance: 118 - 119: 11.036 distance: 118 - 123: 11.075 distance: 119 - 167: 5.969 distance: 120 - 121: 5.253 distance: 120 - 122: 11.679 distance: 123 - 124: 8.759 distance: 124 - 125: 10.889 distance: 125 - 126: 11.232 distance: 125 - 127: 7.450 distance: 127 - 128: 10.202 distance: 128 - 129: 8.418 distance: 128 - 131: 17.784 distance: 129 - 130: 6.847 distance: 129 - 133: 7.323 distance: 131 - 132: 22.926 distance: 133 - 134: 21.385 distance: 134 - 135: 4.856 distance: 134 - 137: 14.672 distance: 135 - 136: 14.929 distance: 135 - 141: 12.863 distance: 137 - 138: 17.042 distance: 138 - 139: 15.095 distance: 138 - 140: 12.454 distance: 141 - 142: 4.153 distance: 142 - 143: 8.291 distance: 142 - 145: 11.402 distance: 143 - 144: 7.045 distance: 143 - 149: 3.845 distance: 145 - 146: 9.445 distance: 146 - 147: 13.384 distance: 146 - 148: 13.901 distance: 149 - 150: 4.618 distance: 150 - 151: 11.379 distance: 150 - 153: 12.104 distance: 151 - 152: 26.528 distance: 151 - 154: 15.057 distance: 154 - 155: 15.959 distance: 155 - 156: 22.869 distance: 155 - 158: 24.886 distance: 156 - 157: 23.810 distance: 156 - 161: 16.527 distance: 158 - 159: 31.109 distance: 158 - 160: 21.628