Starting phenix.real_space_refine on Sat Aug 23 01:22:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vms_21243/08_2025/6vms_21243.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vms_21243/08_2025/6vms_21243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vms_21243/08_2025/6vms_21243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vms_21243/08_2025/6vms_21243.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vms_21243/08_2025/6vms_21243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vms_21243/08_2025/6vms_21243.map" } resolution = 3.8 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= 0.003 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 65 5.16 5 C 5705 2.51 5 N 1512 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 8953 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1823 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 454 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "E" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1782 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2244 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'08Y': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.76, per 1000 atoms: 0.20 Number of scatterers: 8953 At special positions: 0 Unit cell: (103.75, 117.86, 128.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 65 16.00 O 1670 8.00 N 1512 7.00 C 5705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS R 399 " - pdb=" SG CYS R 401 " distance=2.04 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: 0.76 Conformation dependent library (CDL) restraints added in 300.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 38.4% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.839A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.527A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.864A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.589A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.518A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.507A pdb=" N ALA C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.668A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'R' and resid 35 through 40 removed outlier: 3.515A pdb=" N LEU R 40 " --> pdb=" O TYR R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 62 removed outlier: 3.547A pdb=" N ILE R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU R 54 " --> pdb=" O PHE R 50 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N CYS R 56 " --> pdb=" O ASN R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 87 removed outlier: 3.555A pdb=" N TYR R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 97 Processing helix chain 'R' and resid 105 through 138 Processing helix chain 'R' and resid 144 through 168 removed outlier: 3.670A pdb=" N LYS R 149 " --> pdb=" O ARG R 145 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ARG R 150 " --> pdb=" O TYR R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 171 No H-bonds generated for 'chain 'R' and resid 169 through 171' Processing helix chain 'R' and resid 186 through 198 removed outlier: 3.675A pdb=" N VAL R 190 " --> pdb=" O ASN R 186 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL R 196 " --> pdb=" O TYR R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 224 removed outlier: 4.453A pdb=" N ASN R 224 " --> pdb=" O ARG R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 363 through 399 removed outlier: 3.526A pdb=" N LYS R 369 " --> pdb=" O GLN R 365 " (cutoff:3.500A) Proline residue: R 388 - end of helix removed outlier: 3.609A pdb=" N ILE R 397 " --> pdb=" O HIS R 393 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS R 398 " --> pdb=" O ILE R 394 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 426 removed outlier: 4.127A pdb=" N TYR R 408 " --> pdb=" O PRO R 404 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA R 410 " --> pdb=" O VAL R 406 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN R 418 " --> pdb=" O LEU R 414 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 430 through 441 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.737A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.527A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.985A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.924A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.804A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.773A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.894A 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: 6.366A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.943A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.624A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.176A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.822A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.822A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1269 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: 1.09 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2875 1.34 - 1.47: 2292 1.47 - 1.60: 3880 1.60 - 1.73: 0 1.73 - 1.86: 94 Bond restraints: 9141 Sorted by residual: bond pdb=" C25 08Y R 601 " pdb=" C29 08Y R 601 " ideal model delta sigma weight residual 1.367 1.403 -0.036 2.00e-02 2.50e+03 3.17e+00 bond pdb=" C LEU R 407 " pdb=" N TYR R 408 " ideal model delta sigma weight residual 1.335 1.351 -0.017 1.25e-02 6.40e+03 1.84e+00 bond pdb=" C2 08Y R 601 " pdb=" O1 08Y R 601 " ideal model delta sigma weight residual 1.398 1.425 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" CB VAL A 342 " pdb=" CG2 VAL A 342 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.36e+00 bond pdb=" CG LEU B 336 " pdb=" CD2 LEU B 336 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.31e+00 ... (remaining 9136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 12050 1.82 - 3.64: 304 3.64 - 5.47: 41 5.47 - 7.29: 5 7.29 - 9.11: 1 Bond angle restraints: 12401 Sorted by residual: angle pdb=" CB LYS C 32 " pdb=" CG LYS C 32 " pdb=" CD LYS C 32 " ideal model delta sigma weight residual 111.30 120.41 -9.11 2.30e+00 1.89e-01 1.57e+01 angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" C MET E 192 " ideal model delta sigma weight residual 110.80 117.44 -6.64 2.13e+00 2.20e-01 9.71e+00 angle pdb=" N ARG R 361 " pdb=" CA ARG R 361 " pdb=" C ARG R 361 " ideal model delta sigma weight residual 110.80 117.11 -6.31 2.13e+00 2.20e-01 8.77e+00 angle pdb=" N GLY E 33 " pdb=" CA GLY E 33 " pdb=" C GLY E 33 " ideal model delta sigma weight residual 112.89 108.41 4.48 1.58e+00 4.01e-01 8.05e+00 angle pdb=" C ILE B 338 " pdb=" N TRP B 339 " pdb=" CA TRP B 339 " ideal model delta sigma weight residual 123.05 126.75 -3.70 1.40e+00 5.10e-01 7.00e+00 ... (remaining 12396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5249 17.47 - 34.94: 195 34.94 - 52.41: 35 52.41 - 69.88: 18 69.88 - 87.35: 6 Dihedral angle restraints: 5503 sinusoidal: 2192 harmonic: 3311 Sorted by residual: dihedral pdb=" CB CYS R 399 " pdb=" SG CYS R 399 " pdb=" SG CYS R 401 " pdb=" CB CYS R 401 " ideal model delta sinusoidal sigma weight residual -86.00 -145.68 59.68 1 1.00e+01 1.00e-02 4.75e+01 dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 149.27 -56.27 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CA PRO R 139 " pdb=" C PRO R 139 " pdb=" N MET R 140 " pdb=" CA MET R 140 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 5500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 765 0.029 - 0.058: 431 0.058 - 0.087: 140 0.087 - 0.116: 70 0.116 - 0.145: 13 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CA ILE A 221 " pdb=" N ILE A 221 " pdb=" C ILE A 221 " pdb=" CB ILE A 221 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA VAL B 135 " pdb=" N VAL B 135 " pdb=" C VAL B 135 " pdb=" CB VAL B 135 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1416 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 08Y R 601 " -0.099 2.00e-02 2.50e+03 8.71e-02 2.28e+02 pdb=" C23 08Y R 601 " 0.157 2.00e-02 2.50e+03 pdb=" C24 08Y R 601 " -0.063 2.00e-02 2.50e+03 pdb=" C25 08Y R 601 " -0.032 2.00e-02 2.50e+03 pdb=" C26 08Y R 601 " -0.107 2.00e-02 2.50e+03 pdb=" C28 08Y R 601 " -0.087 2.00e-02 2.50e+03 pdb=" C29 08Y R 601 " -0.021 2.00e-02 2.50e+03 pdb=" C30 08Y R 601 " 0.092 2.00e-02 2.50e+03 pdb=" C31 08Y R 601 " 0.023 2.00e-02 2.50e+03 pdb=" C32 08Y R 601 " 0.122 2.00e-02 2.50e+03 pdb=" N5 08Y R 601 " -0.056 2.00e-02 2.50e+03 pdb="BR 08Y R 601 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 08Y R 601 " 0.060 2.00e-02 2.50e+03 5.54e-02 4.61e+01 pdb=" C3 08Y R 601 " -0.071 2.00e-02 2.50e+03 pdb=" C6 08Y R 601 " -0.074 2.00e-02 2.50e+03 pdb=" C9 08Y R 601 " 0.008 2.00e-02 2.50e+03 pdb=" N2 08Y R 601 " 0.011 2.00e-02 2.50e+03 pdb=" O4 08Y R 601 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 08Y R 601 " -0.067 2.00e-02 2.50e+03 4.51e-02 3.05e+01 pdb=" C3 08Y R 601 " 0.035 2.00e-02 2.50e+03 pdb=" C5 08Y R 601 " 0.055 2.00e-02 2.50e+03 pdb=" C8 08Y R 601 " -0.000 2.00e-02 2.50e+03 pdb=" N1 08Y R 601 " 0.028 2.00e-02 2.50e+03 pdb=" O3 08Y R 601 " -0.051 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 112 2.65 - 3.21: 8326 3.21 - 3.77: 13346 3.77 - 4.34: 19193 4.34 - 4.90: 31065 Nonbonded interactions: 72042 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.082 3.040 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.103 3.040 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.116 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.126 3.040 nonbonded pdb=" OG SER E 106 " pdb=" OH TYR E 190 " model vdw 2.227 3.040 ... (remaining 72037 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.190 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 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 0.039 9145 Z= 0.201 Angle : 0.706 9.108 12409 Z= 0.394 Chirality : 0.043 0.145 1419 Planarity : 0.005 0.087 1557 Dihedral : 11.035 87.351 3353 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.27 (0.24), residues: 1121 helix: -0.49 (0.24), residues: 380 sheet: 0.63 (0.29), residues: 275 loop : -0.23 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 314 TYR 0.012 0.002 TYR R 146 PHE 0.016 0.002 PHE B 234 TRP 0.025 0.003 TRP B 82 HIS 0.005 0.001 HIS R 106 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 9141) covalent geometry : angle 0.70438 (12401) SS BOND : bond 0.00368 ( 4) SS BOND : angle 1.92235 ( 8) hydrogen bonds : bond 0.16323 ( 449) hydrogen bonds : angle 7.69191 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.7739 (t80) cc_final: 0.7508 (t80) REVERT: A 228 SER cc_start: 0.7575 (p) cc_final: 0.6988 (p) REVERT: A 273 LEU cc_start: 0.8501 (mt) cc_final: 0.8101 (tt) REVERT: B 76 ASP cc_start: 0.6632 (t0) cc_final: 0.6373 (t0) REVERT: B 171 ILE cc_start: 0.7446 (tp) cc_final: 0.7173 (tp) REVERT: E 60 TYR cc_start: 0.7906 (m-80) cc_final: 0.7482 (m-80) REVERT: E 68 PHE cc_start: 0.7615 (m-10) cc_final: 0.7041 (m-10) REVERT: E 71 SER cc_start: 0.6618 (t) cc_final: 0.6020 (p) REVERT: E 83 MET cc_start: 0.8704 (mtt) cc_final: 0.8474 (mtm) REVERT: E 234 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7945 (mm-30) REVERT: R 164 PHE cc_start: 0.7718 (t80) cc_final: 0.7498 (t80) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.1086 time to fit residues: 44.0854 Evaluate side-chains 175 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 220 GLN B 266 HIS B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN C 44 HIS ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN R 106 HIS R 179 GLN ** R 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.172523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144409 restraints weight = 12257.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144691 restraints weight = 12992.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.146038 restraints weight = 10853.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.146362 restraints weight = 8748.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.146821 restraints weight = 7900.993| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9145 Z= 0.163 Angle : 0.666 7.778 12409 Z= 0.358 Chirality : 0.046 0.196 1419 Planarity : 0.005 0.055 1557 Dihedral : 5.736 65.439 1312 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.06 % Allowed : 11.43 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.73 (0.25), residues: 1121 helix: 0.80 (0.26), residues: 393 sheet: 0.85 (0.29), residues: 277 loop : 0.12 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 314 TYR 0.019 0.002 TYR B 59 PHE 0.028 0.002 PHE R 390 TRP 0.019 0.002 TRP R 100 HIS 0.014 0.002 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9141) covalent geometry : angle 0.66393 (12401) SS BOND : bond 0.00452 ( 4) SS BOND : angle 2.07852 ( 8) hydrogen bonds : bond 0.04497 ( 449) hydrogen bonds : angle 5.50946 ( 1269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.8230 (mt) cc_final: 0.7857 (tt) REVERT: A 345 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7901 (mttm) REVERT: B 59 TYR cc_start: 0.8499 (m-80) cc_final: 0.8200 (m-80) REVERT: B 76 ASP cc_start: 0.6536 (t0) cc_final: 0.6268 (t0) REVERT: B 188 MET cc_start: 0.8601 (mmm) cc_final: 0.8321 (mmm) REVERT: B 191 SER cc_start: 0.8132 (t) cc_final: 0.7906 (t) REVERT: B 266 HIS cc_start: 0.6341 (t-170) cc_final: 0.6038 (t70) REVERT: B 334 SER cc_start: 0.8194 (m) cc_final: 0.7918 (p) outliers start: 30 outliers final: 17 residues processed: 226 average time/residue: 0.1214 time to fit residues: 36.0844 Evaluate side-chains 183 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Chi-restraints excluded: chain R residue 433 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 0.0670 chunk 85 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** R 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.166878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135207 restraints weight = 12339.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136415 restraints weight = 11614.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137470 restraints weight = 9287.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.137721 restraints weight = 8095.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140635 restraints weight = 7071.380| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9145 Z= 0.125 Angle : 0.589 8.305 12409 Z= 0.316 Chirality : 0.044 0.166 1419 Planarity : 0.004 0.038 1557 Dihedral : 5.454 62.064 1312 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.04 % Allowed : 13.67 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.78 (0.25), residues: 1121 helix: 1.18 (0.27), residues: 392 sheet: 0.71 (0.29), residues: 269 loop : -0.06 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 217 TYR 0.019 0.001 TYR A 287 PHE 0.021 0.002 PHE R 172 TRP 0.023 0.002 TRP R 100 HIS 0.009 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9141) covalent geometry : angle 0.58840 (12401) SS BOND : bond 0.00430 ( 4) SS BOND : angle 1.48806 ( 8) hydrogen bonds : bond 0.03853 ( 449) hydrogen bonds : angle 5.23038 ( 1269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.8271 (mt) cc_final: 0.7943 (tt) REVERT: B 10 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6753 (pt0) REVERT: B 76 ASP cc_start: 0.6477 (t0) cc_final: 0.6206 (t0) REVERT: B 175 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7254 (mm110) REVERT: B 334 SER cc_start: 0.8389 (m) cc_final: 0.8185 (p) REVERT: E 192 MET cc_start: 0.8477 (ptt) cc_final: 0.8094 (ptt) REVERT: R 93 TYR cc_start: 0.7235 (t80) cc_final: 0.6693 (t80) REVERT: R 100 TRP cc_start: 0.4919 (t60) cc_final: 0.3892 (t60) REVERT: R 220 ARG cc_start: 0.5884 (ttt-90) cc_final: 0.5384 (ttt90) outliers start: 20 outliers final: 13 residues processed: 198 average time/residue: 0.1028 time to fit residues: 27.6066 Evaluate side-chains 168 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Chi-restraints excluded: chain R residue 433 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.159324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.127107 restraints weight = 12236.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.128755 restraints weight = 11118.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130433 restraints weight = 9207.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130774 restraints weight = 6952.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131164 restraints weight = 6491.072| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9145 Z= 0.166 Angle : 0.601 6.473 12409 Z= 0.320 Chirality : 0.045 0.196 1419 Planarity : 0.004 0.040 1557 Dihedral : 5.371 60.432 1312 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.37 % Allowed : 14.59 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.74 (0.25), residues: 1121 helix: 1.40 (0.28), residues: 383 sheet: 0.42 (0.28), residues: 291 loop : -0.14 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 217 TYR 0.017 0.001 TYR E 190 PHE 0.019 0.002 PHE R 389 TRP 0.013 0.002 TRP R 100 HIS 0.004 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9141) covalent geometry : angle 0.60046 (12401) SS BOND : bond 0.00330 ( 4) SS BOND : angle 1.50300 ( 8) hydrogen bonds : bond 0.03796 ( 449) hydrogen bonds : angle 5.03095 ( 1269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7611 (m-30) cc_final: 0.7298 (m-30) REVERT: A 33 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7381 (mt-10) REVERT: A 273 LEU cc_start: 0.8234 (mt) cc_final: 0.7976 (tt) REVERT: A 313 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7214 (mtm-85) REVERT: B 76 ASP cc_start: 0.6568 (t0) cc_final: 0.6329 (t0) REVERT: B 88 ASN cc_start: 0.8406 (m-40) cc_final: 0.8122 (m110) REVERT: B 175 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7432 (mm110) REVERT: E 192 MET cc_start: 0.8596 (ptt) cc_final: 0.8070 (ptt) REVERT: R 108 ASP cc_start: 0.6561 (m-30) cc_final: 0.6200 (m-30) REVERT: R 148 SER cc_start: 0.8752 (m) cc_final: 0.8113 (t) REVERT: R 403 ILE cc_start: 0.8096 (tp) cc_final: 0.7532 (mm) outliers start: 33 outliers final: 22 residues processed: 205 average time/residue: 0.1121 time to fit residues: 31.0692 Evaluate side-chains 192 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Chi-restraints excluded: chain R residue 433 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.160107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128517 restraints weight = 12118.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.129075 restraints weight = 11790.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.130339 restraints weight = 9928.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130471 restraints weight = 8476.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131163 restraints weight = 7538.895| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9145 Z= 0.142 Angle : 0.583 8.324 12409 Z= 0.310 Chirality : 0.044 0.177 1419 Planarity : 0.004 0.040 1557 Dihedral : 5.259 57.010 1312 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.47 % Allowed : 16.22 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.55 (0.25), residues: 1121 helix: 1.31 (0.28), residues: 384 sheet: 0.28 (0.28), residues: 291 loop : -0.31 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 220 TYR 0.017 0.001 TYR E 190 PHE 0.020 0.002 PHE R 390 TRP 0.015 0.001 TRP R 100 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9141) covalent geometry : angle 0.58189 (12401) SS BOND : bond 0.00292 ( 4) SS BOND : angle 1.39064 ( 8) hydrogen bonds : bond 0.03639 ( 449) hydrogen bonds : angle 4.94234 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7711 (m-30) cc_final: 0.7407 (m-30) REVERT: A 228 SER cc_start: 0.7574 (OUTLIER) cc_final: 0.7212 (t) REVERT: A 273 LEU cc_start: 0.8347 (mt) cc_final: 0.8130 (tt) REVERT: A 313 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7251 (mtm-85) REVERT: B 76 ASP cc_start: 0.6592 (t0) cc_final: 0.6313 (t0) REVERT: B 88 ASN cc_start: 0.8489 (m-40) cc_final: 0.8234 (m110) REVERT: B 175 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7546 (mm110) REVERT: C 11 GLN cc_start: 0.6237 (mp10) cc_final: 0.4775 (mt0) REVERT: E 93 MET cc_start: 0.8663 (tpp) cc_final: 0.8057 (ttt) REVERT: E 192 MET cc_start: 0.8607 (ptt) cc_final: 0.7950 (ptt) REVERT: R 108 ASP cc_start: 0.6653 (m-30) cc_final: 0.6363 (m-30) outliers start: 34 outliers final: 23 residues processed: 203 average time/residue: 0.1171 time to fit residues: 31.5212 Evaluate side-chains 192 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 219 ARG Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Chi-restraints excluded: chain R residue 433 PHE 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: 56.9844 > 50: distance: 99 - 245: 8.056 distance: 122 - 238: 7.495 distance: 125 - 235: 13.112 distance: 152 - 207: 8.040 distance: 170 - 177: 30.370 distance: 177 - 178: 33.116 distance: 178 - 179: 34.118 distance: 178 - 181: 24.664 distance: 179 - 180: 32.605 distance: 179 - 189: 41.705 distance: 181 - 182: 26.693 distance: 182 - 183: 8.951 distance: 182 - 184: 16.369 distance: 183 - 185: 7.894 distance: 184 - 186: 11.096 distance: 185 - 187: 5.849 distance: 186 - 187: 3.839 distance: 189 - 190: 13.312 distance: 189 - 195: 19.487 distance: 190 - 191: 29.517 distance: 190 - 193: 16.142 distance: 191 - 192: 29.313 distance: 191 - 196: 9.180 distance: 193 - 194: 32.321 distance: 194 - 195: 34.889 distance: 196 - 197: 36.096 distance: 197 - 198: 20.009 distance: 197 - 200: 33.125 distance: 198 - 199: 21.162 distance: 198 - 204: 11.090 distance: 200 - 201: 28.631 distance: 201 - 202: 37.487 distance: 201 - 203: 28.277 distance: 204 - 205: 11.572 distance: 205 - 206: 12.343 distance: 205 - 208: 9.190 distance: 206 - 207: 11.208 distance: 206 - 211: 14.508 distance: 208 - 209: 21.405 distance: 208 - 210: 21.385 distance: 211 - 212: 12.867 distance: 212 - 213: 11.441 distance: 212 - 215: 7.031 distance: 213 - 214: 9.294 distance: 213 - 222: 15.463 distance: 215 - 216: 13.681 distance: 216 - 217: 6.677 distance: 216 - 218: 9.079 distance: 217 - 219: 9.354 distance: 218 - 220: 10.640 distance: 219 - 221: 5.706 distance: 222 - 223: 6.713 distance: 223 - 224: 16.677 distance: 224 - 225: 17.184 distance: 224 - 226: 6.800 distance: 227 - 228: 18.433 distance: 227 - 230: 23.201 distance: 228 - 229: 13.823 distance: 228 - 231: 12.145 distance: 231 - 232: 8.884 distance: 232 - 233: 17.216 distance: 233 - 234: 7.753 distance: 233 - 235: 17.020 distance: 235 - 236: 11.227 distance: 236 - 237: 15.240 distance: 236 - 239: 14.195 distance: 237 - 238: 8.631 distance: 237 - 242: 12.693 distance: 239 - 240: 37.908 distance: 239 - 241: 34.843 distance: 242 - 243: 12.693 distance: 243 - 244: 7.870 distance: 243 - 246: 5.168 distance: 244 - 245: 6.837 distance: 244 - 251: 7.328 distance: 246 - 247: 22.632 distance: 247 - 248: 12.110 distance: 249 - 250: 4.027