Starting phenix.real_space_refine on Wed Feb 4 05:17:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vcb_21147/02_2026/6vcb_21147_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vcb_21147/02_2026/6vcb_21147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vcb_21147/02_2026/6vcb_21147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vcb_21147/02_2026/6vcb_21147.map" model { file = "/net/cci-nas-00/data/ceres_data/6vcb_21147/02_2026/6vcb_21147_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vcb_21147/02_2026/6vcb_21147_neut.cif" } resolution = 3.3 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= 0.004 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 S 54 5.16 5 Cl 2 4.86 5 C 5787 2.51 5 N 1573 2.21 5 O 1658 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9074 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3000 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 14, 'TRANS': 363} Chain breaks: 3 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 5, 'GLU:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "P" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 231 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 30} 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: "A" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1810 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 5 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "N" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'QW7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.10, per 1000 atoms: 0.23 Number of scatterers: 9074 At special positions: 0 Unit cell: (166.4, 102.96, 98.8, 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) Cl 2 17.00 S 54 16.00 O 1658 8.00 N 1573 7.00 C 5787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.02 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: 0.53 Conformation dependent library (CDL) restraints added in 231.7 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2180 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 42.1% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'R' and resid 31 through 51 removed outlier: 3.917A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 93 removed outlier: 4.439A pdb=" N SER R 93 " --> pdb=" O PRO R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 168 removed outlier: 3.681A pdb=" N LEU R 142 " --> pdb=" O GLU R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 206 Processing helix chain 'R' and resid 216 through 223 removed outlier: 3.898A pdb=" N ASP R 222 " --> pdb=" O LEU R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 256 Processing helix chain 'R' and resid 261 through 274 removed outlier: 3.638A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 291 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 303 through 336 removed outlier: 4.504A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 368 removed outlier: 3.691A pdb=" N ALA R 368 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 393 removed outlier: 4.028A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 402 Processing helix chain 'R' and resid 406 through 421 Processing helix chain 'P' and resid 8 through 34 removed outlier: 3.681A pdb=" N LYS P 34 " --> pdb=" O ALA P 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 38 Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.770A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.115A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.836A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.587A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 removed outlier: 3.575A pdb=" N GLN B 32 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 4.116A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.936A 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 'N' and resid 28 through 32 removed outlier: 3.646A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.606A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.094A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'R' and resid 79 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.861A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.747A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.040A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.741A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.707A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.495A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.259A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'N' and resid 59 through 60 removed outlier: 6.450A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1314 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: 1.45 Time building geometry restraints manager: 0.71 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: 2908 1.34 - 1.46: 2128 1.46 - 1.58: 4167 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 9277 Sorted by residual: bond pdb=" C17 QW7 R 501 " pdb=" C18 QW7 R 501 " ideal model delta sigma weight residual 1.490 1.391 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" CG LEU R 159 " pdb=" CD1 LEU R 159 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.06e+00 bond pdb=" C03 QW7 R 501 " pdb=" O02 QW7 R 501 " ideal model delta sigma weight residual 1.349 1.400 -0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" CG LEU R 159 " pdb=" CD2 LEU R 159 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.08e+00 bond pdb=" C26 QW7 R 501 " pdb=" C27 QW7 R 501 " ideal model delta sigma weight residual 1.528 1.483 0.045 2.00e-02 2.50e+03 5.02e+00 ... (remaining 9272 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 12449 3.65 - 7.30: 125 7.30 - 10.95: 16 10.95 - 14.60: 2 14.60 - 18.25: 1 Bond angle restraints: 12593 Sorted by residual: angle pdb=" CA LEU A 46 " pdb=" CB LEU A 46 " pdb=" CG LEU A 46 " ideal model delta sigma weight residual 116.30 134.55 -18.25 3.50e+00 8.16e-02 2.72e+01 angle pdb=" C ARG R 299 " pdb=" N ASN R 300 " pdb=" CA ASN R 300 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 angle pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " pdb=" CG LEU B 336 " ideal model delta sigma weight residual 116.30 130.74 -14.44 3.50e+00 8.16e-02 1.70e+01 angle pdb=" C ILE R 147 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 121.14 114.24 6.90 1.75e+00 3.27e-01 1.56e+01 ... (remaining 12588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 5047 15.42 - 30.84: 317 30.84 - 46.26: 89 46.26 - 61.68: 12 61.68 - 77.11: 8 Dihedral angle restraints: 5473 sinusoidal: 2106 harmonic: 3367 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -152.86 66.86 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 145.59 -52.59 1 1.00e+01 1.00e-02 3.77e+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 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 5470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1046 0.063 - 0.126: 305 0.126 - 0.190: 36 0.190 - 0.253: 12 0.253 - 0.316: 5 Chirality restraints: 1404 Sorted by residual: chirality pdb=" C09 QW7 R 501 " pdb=" C08 QW7 R 501 " pdb=" C10 QW7 R 501 " pdb=" N11 QW7 R 501 " both_signs ideal model delta sigma weight residual False -2.29 -2.60 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CG LEU A 44 " pdb=" CB LEU A 44 " pdb=" CD1 LEU A 44 " pdb=" CD2 LEU A 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CG LEU R 183 " pdb=" CB LEU R 183 " pdb=" CD1 LEU R 183 " pdb=" CD2 LEU R 183 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1401 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 242 " -0.018 2.00e-02 2.50e+03 1.75e-02 6.10e+00 pdb=" CG TYR R 242 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR R 242 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR R 242 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR R 242 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR R 242 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR R 242 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 242 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 169 " 0.021 2.00e-02 2.50e+03 1.50e-02 5.63e+00 pdb=" CG TRP B 169 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 169 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 169 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 169 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 169 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 169 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 282 " -0.039 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO R 283 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO R 283 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 283 " -0.033 5.00e-02 4.00e+02 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 192 2.67 - 3.23: 8324 3.23 - 3.79: 14865 3.79 - 4.34: 19328 4.34 - 4.90: 31834 Nonbonded interactions: 74543 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.117 3.040 nonbonded pdb=" OD2 ASP B 212 " pdb=" NH2 ARG B 219 " model vdw 2.145 3.120 nonbonded pdb=" OE2 GLU N 6 " pdb=" N GLY N 121 " model vdw 2.159 3.120 nonbonded pdb=" NE2 HIS A 362 " pdb=" OD2 ASP A 378 " model vdw 2.160 3.120 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.222 3.040 ... (remaining 74538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.360 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 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 : 0.007 0.099 9283 Z= 0.284 Angle : 1.007 18.255 12605 Z= 0.532 Chirality : 0.061 0.316 1404 Planarity : 0.007 0.058 1599 Dihedral : 11.588 77.105 3275 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.85 % Allowed : 5.32 % Favored : 93.82 % 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 are not related in a simple way. whole: -4.29 (0.19), residues: 1130 helix: -2.61 (0.17), residues: 456 sheet: -2.38 (0.30), residues: 218 loop : -3.17 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 118 TYR 0.041 0.004 TYR R 242 PHE 0.021 0.003 PHE R 280 TRP 0.041 0.004 TRP B 169 HIS 0.010 0.002 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00655 ( 9277) covalent geometry : angle 1.00638 (12593) SS BOND : bond 0.00437 ( 6) SS BOND : angle 1.77997 ( 12) hydrogen bonds : bond 0.11091 ( 464) hydrogen bonds : angle 6.70915 ( 1314) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 267 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 262 GLU cc_start: 0.7641 (tp30) cc_final: 0.7356 (mt-10) REVERT: R 304 ASN cc_start: 0.7541 (m-40) cc_final: 0.6142 (t0) REVERT: R 372 ASP cc_start: 0.8600 (m-30) cc_final: 0.7945 (m-30) REVERT: R 417 TRP cc_start: 0.6373 (t-100) cc_final: 0.6064 (t-100) REVERT: P 18 SER cc_start: 0.8125 (m) cc_final: 0.7828 (p) REVERT: P 27 GLU cc_start: 0.7702 (tt0) cc_final: 0.7384 (tt0) REVERT: A 338 LYS cc_start: 0.8594 (ttpm) cc_final: 0.8278 (ttpp) REVERT: B 211 TRP cc_start: 0.8795 (m100) cc_final: 0.8570 (m100) REVERT: B 335 PHE cc_start: 0.7892 (m-80) cc_final: 0.7673 (m-10) REVERT: G 19 LEU cc_start: 0.8822 (mt) cc_final: 0.8493 (mt) REVERT: G 46 LYS cc_start: 0.8561 (mppt) cc_final: 0.8351 (mmtm) REVERT: G 48 ASP cc_start: 0.8561 (t70) cc_final: 0.8201 (t0) REVERT: N 82 GLN cc_start: 0.7274 (tp-100) cc_final: 0.7039 (tp-100) REVERT: N 105 ARG cc_start: 0.6366 (mtp-110) cc_final: 0.6160 (mtp-110) outliers start: 8 outliers final: 4 residues processed: 274 average time/residue: 0.0986 time to fit residues: 35.4878 Evaluate side-chains 172 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 168 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain A residue 43 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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: 55.2695 > 50: distance: 54 - 57: 11.679 distance: 57 - 58: 4.285 distance: 58 - 59: 6.087 distance: 58 - 61: 10.682 distance: 59 - 60: 16.904 distance: 59 - 62: 9.851 distance: 62 - 63: 5.801 distance: 62 - 167: 9.563 distance: 63 - 64: 9.068 distance: 63 - 66: 21.888 distance: 64 - 65: 10.309 distance: 65 - 164: 10.286 distance: 67 - 68: 5.861 distance: 68 - 69: 8.603 distance: 68 - 71: 15.309 distance: 69 - 70: 6.129 distance: 69 - 72: 10.329 distance: 72 - 73: 6.852 distance: 73 - 74: 10.712 distance: 73 - 76: 7.369 distance: 74 - 75: 8.086 distance: 74 - 78: 7.078 distance: 76 - 77: 9.516 distance: 77 - 181: 8.273 distance: 78 - 79: 7.229 distance: 78 - 84: 13.641 distance: 79 - 80: 17.094 distance: 79 - 82: 25.916 distance: 80 - 81: 19.131 distance: 80 - 85: 17.098 distance: 82 - 83: 23.527 distance: 83 - 84: 10.614 distance: 85 - 86: 10.931 distance: 86 - 87: 10.796 distance: 86 - 89: 9.283 distance: 87 - 88: 5.963 distance: 87 - 99: 3.279 distance: 89 - 90: 6.864 distance: 90 - 91: 12.977 distance: 90 - 92: 5.336 distance: 91 - 93: 3.169 distance: 92 - 94: 7.062 distance: 92 - 95: 13.886 distance: 93 - 94: 13.313 distance: 94 - 96: 13.594 distance: 95 - 97: 7.544 distance: 96 - 98: 8.852 distance: 97 - 98: 9.297 distance: 99 - 100: 7.533 distance: 100 - 101: 3.888 distance: 100 - 103: 7.292 distance: 101 - 111: 6.610 distance: 103 - 104: 9.331 distance: 104 - 105: 7.688 distance: 104 - 106: 5.650 distance: 105 - 107: 6.380 distance: 106 - 108: 7.022 distance: 107 - 109: 4.933 distance: 108 - 109: 6.862 distance: 109 - 110: 3.547 distance: 111 - 112: 5.628 distance: 112 - 115: 4.057 distance: 113 - 116: 3.286 distance: 114 - 137: 5.477 distance: 116 - 117: 4.867 distance: 116 - 122: 9.051 distance: 117 - 120: 5.746 distance: 118 - 119: 3.481 distance: 118 - 123: 3.156 distance: 120 - 121: 8.337 distance: 121 - 122: 10.818 distance: 124 - 125: 3.249 distance: 124 - 127: 4.242 distance: 125 - 126: 3.040 distance: 127 - 128: 3.702 distance: 128 - 130: 7.273 distance: 129 - 131: 4.773 distance: 130 - 132: 5.496 distance: 130 - 133: 4.815 distance: 131 - 132: 5.125 distance: 134 - 136: 4.354