Starting phenix.real_space_refine on Fri Aug 22 21:53:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rmg_24569/08_2025/7rmg_24569.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rmg_24569/08_2025/7rmg_24569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rmg_24569/08_2025/7rmg_24569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rmg_24569/08_2025/7rmg_24569.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rmg_24569/08_2025/7rmg_24569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rmg_24569/08_2025/7rmg_24569.map" } resolution = 3.0 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= 0.004 sd= 0.412 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1082 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 4737 2.51 5 N 1226 2.21 5 O 1300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 7316 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1510 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 2, 'ARG:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 71 Chain: "R" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2306 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 14, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 43 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 8} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2319 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 7, 'ASP:plan': 13, 'ASN:plan1': 5, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "G" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 245 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "N" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 851 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 1.98, per 1000 atoms: 0.27 Number of scatterers: 7316 At special positions: 0 Unit cell: (70.14, 96.86, 131.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1300 8.00 N 1226 7.00 C 4737 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 180 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 476.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1838 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 11 sheets defined 39.4% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 25 through 38 removed outlier: 3.515A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.626A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 316 removed outlier: 4.080A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.587A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.553A pdb=" N ARG A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 60 removed outlier: 3.988A pdb=" N ILE R 42 " --> pdb=" O ALA R 38 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS R 60 " --> pdb=" O ILE R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 96 removed outlier: 4.352A pdb=" N HIS R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 136 removed outlier: 4.233A pdb=" N TYR R 104 " --> pdb=" O TYR R 100 " (cutoff:3.500A) Proline residue: R 112 - end of helix Processing helix chain 'R' and resid 143 through 168 Proline residue: R 164 - end of helix Processing helix chain 'R' and resid 190 through 225 removed outlier: 5.024A pdb=" N LEU R 207 " --> pdb=" O LEU R 203 " (cutoff:3.500A) Proline residue: R 208 - end of helix removed outlier: 3.586A pdb=" N ALA R 225 " --> pdb=" O ILE R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 270 removed outlier: 3.646A pdb=" N LYS R 243 " --> pdb=" O GLN R 239 " (cutoff:3.500A) Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 271 through 273 No H-bonds generated for 'chain 'R' and resid 271 through 273' Processing helix chain 'R' and resid 274 through 280 removed outlier: 3.907A pdb=" N LEU R 277 " --> pdb=" O ASN R 274 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR R 278 " --> pdb=" O PRO R 275 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU R 279 " --> pdb=" O ASP R 276 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS R 280 " --> pdb=" O LEU R 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 274 through 280' Processing helix chain 'R' and resid 281 through 296 Processing helix chain 'R' and resid 299 through 309 removed outlier: 3.915A pdb=" N ILE R 303 " --> pdb=" O MET R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 320 Processing helix chain 'B' and resid 15 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.832A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.577A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.768A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.389A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 169 through 174 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.988A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.652A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.600A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.993A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.759A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.953A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.596A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.165A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1098 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: 1.18 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1362 1.33 - 1.45: 2058 1.45 - 1.58: 3997 1.58 - 1.71: 0 1.71 - 1.83: 75 Bond restraints: 7492 Sorted by residual: bond pdb=" C ILE A 382 " pdb=" O ILE A 382 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.19e-02 7.06e+03 8.43e+00 bond pdb=" N ILE B 58 " pdb=" CA ILE B 58 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.66e+00 bond pdb=" C ASP A 381 " pdb=" O ASP A 381 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.26e-02 6.30e+03 7.24e+00 bond pdb=" N ILE A 382 " pdb=" CA ILE A 382 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.21e-02 6.83e+03 7.09e+00 bond pdb=" C ILE B 58 " pdb=" O ILE B 58 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.20e-02 6.94e+03 6.84e+00 ... (remaining 7487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 9839 1.73 - 3.46: 313 3.46 - 5.20: 55 5.20 - 6.93: 11 6.93 - 8.66: 8 Bond angle restraints: 10226 Sorted by residual: angle pdb=" CA ILE A 382 " pdb=" C ILE A 382 " pdb=" O ILE A 382 " ideal model delta sigma weight residual 120.85 116.82 4.03 1.06e+00 8.90e-01 1.45e+01 angle pdb=" O ILE A 382 " pdb=" C ILE A 382 " pdb=" N ILE A 383 " ideal model delta sigma weight residual 121.83 125.41 -3.58 1.03e+00 9.43e-01 1.21e+01 angle pdb=" O LYS A 380 " pdb=" C LYS A 380 " pdb=" N ASP A 381 " ideal model delta sigma weight residual 122.12 118.52 3.60 1.06e+00 8.90e-01 1.15e+01 angle pdb=" N PHE R 111 " pdb=" CA PHE R 111 " pdb=" C PHE R 111 " ideal model delta sigma weight residual 109.81 117.17 -7.36 2.21e+00 2.05e-01 1.11e+01 angle pdb=" CA LYS A 380 " pdb=" C LYS A 380 " pdb=" N ASP A 381 " ideal model delta sigma weight residual 117.30 121.10 -3.80 1.16e+00 7.43e-01 1.08e+01 ... (remaining 10221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 3968 16.21 - 32.41: 294 32.41 - 48.61: 50 48.61 - 64.82: 11 64.82 - 81.02: 9 Dihedral angle restraints: 4332 sinusoidal: 1495 harmonic: 2837 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+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 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA TYR R 205 " pdb=" C TYR R 205 " pdb=" N PHE R 206 " pdb=" CA PHE R 206 " ideal model delta harmonic sigma weight residual 180.00 -160.45 -19.55 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 4329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 786 0.041 - 0.082: 272 0.082 - 0.123: 99 0.123 - 0.165: 31 0.165 - 0.206: 6 Chirality restraints: 1194 Sorted by residual: chirality pdb=" CB ILE B 58 " pdb=" CA ILE B 58 " pdb=" CG1 ILE B 58 " pdb=" CG2 ILE B 58 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE A 382 " pdb=" CA ILE A 382 " pdb=" CG1 ILE A 382 " pdb=" CG2 ILE A 382 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB ILE A 383 " pdb=" CA ILE A 383 " pdb=" CG1 ILE A 383 " pdb=" CG2 ILE A 383 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1191 not shown) Planarity restraints: 1275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.17e+00 pdb=" N PRO B 236 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 82 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C ALA R 82 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA R 82 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA R 83 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 241 " 0.013 2.00e-02 2.50e+03 1.95e-02 6.62e+00 pdb=" CG PHE B 241 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE B 241 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 241 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE B 241 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 241 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 241 " -0.001 2.00e-02 2.50e+03 ... (remaining 1272 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2015 2.81 - 3.33: 6111 3.33 - 3.86: 12100 3.86 - 4.38: 14013 4.38 - 4.90: 25013 Nonbonded interactions: 59252 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.290 3.040 nonbonded pdb=" O ALA R 36 " pdb=" OG1 THR R 40 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.315 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.322 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.349 3.040 ... (remaining 59247 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.810 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:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 7496 Z= 0.242 Angle : 0.758 8.659 10232 Z= 0.432 Chirality : 0.051 0.206 1194 Planarity : 0.006 0.067 1275 Dihedral : 12.654 81.023 2485 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.25), residues: 942 helix: -0.67 (0.24), residues: 352 sheet: 0.38 (0.34), residues: 211 loop : -0.97 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.020 0.002 TYR R 92 PHE 0.044 0.002 PHE B 241 TRP 0.018 0.002 TRP B 99 HIS 0.015 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 7492) covalent geometry : angle 0.75693 (10226) SS BOND : bond 0.00345 ( 3) SS BOND : angle 2.03747 ( 6) hydrogen bonds : bond 0.14290 ( 383) hydrogen bonds : angle 6.65646 ( 1098) Misc. bond : bond 0.10119 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.277 Fit side-chains REVERT: A 272 ASP cc_start: 0.6554 (m-30) cc_final: 0.5659 (m-30) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.4347 time to fit residues: 69.1285 Evaluate side-chains 108 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 67.423 > 50: distance: 98 - 115: 33.681 distance: 102 - 129: 22.362 distance: 106 - 137: 27.944 distance: 109 - 115: 34.608 distance: 110 - 142: 27.149 distance: 115 - 116: 56.289 distance: 116 - 117: 40.358 distance: 116 - 119: 40.212 distance: 117 - 118: 41.353 distance: 117 - 129: 39.689 distance: 118 - 150: 43.096 distance: 119 - 120: 27.893 distance: 120 - 121: 20.481 distance: 120 - 122: 23.776 distance: 121 - 123: 9.722 distance: 122 - 124: 22.954 distance: 122 - 125: 13.303 distance: 123 - 124: 25.819 distance: 124 - 126: 15.120 distance: 125 - 127: 10.801 distance: 126 - 128: 8.588 distance: 127 - 128: 6.338 distance: 129 - 130: 11.815 distance: 130 - 131: 22.844 distance: 130 - 133: 43.828 distance: 131 - 132: 53.080 distance: 131 - 137: 54.148 distance: 133 - 134: 50.010 distance: 134 - 135: 54.558 distance: 134 - 136: 42.962 distance: 137 - 138: 49.992 distance: 138 - 139: 39.743 distance: 138 - 141: 40.784 distance: 139 - 140: 56.332 distance: 139 - 142: 27.556 distance: 142 - 143: 26.608 distance: 143 - 144: 13.575 distance: 143 - 146: 23.748 distance: 144 - 145: 24.688 distance: 144 - 150: 20.869 distance: 146 - 147: 26.770 distance: 147 - 148: 15.050 distance: 148 - 149: 12.196 distance: 150 - 151: 54.171 distance: 151 - 152: 42.731 distance: 151 - 154: 16.921 distance: 152 - 153: 11.631 distance: 152 - 156: 59.057 distance: 154 - 155: 33.501 distance: 156 - 157: 11.284 distance: 157 - 158: 4.743 distance: 157 - 160: 16.859 distance: 158 - 159: 54.180 distance: 158 - 162: 4.105 distance: 160 - 161: 52.709 distance: 162 - 163: 12.103 distance: 163 - 164: 49.988 distance: 163 - 166: 41.157 distance: 164 - 165: 35.352 distance: 164 - 169: 22.210 distance: 166 - 167: 19.738 distance: 166 - 168: 28.678 distance: 169 - 170: 44.121 distance: 170 - 171: 32.703 distance: 170 - 173: 7.189 distance: 171 - 172: 38.327 distance: 171 - 177: 22.021 distance: 173 - 174: 57.272 distance: 174 - 175: 13.549 distance: 175 - 176: 26.121 distance: 177 - 178: 44.357 distance: 178 - 179: 27.995 distance: 178 - 181: 36.058 distance: 179 - 180: 62.706 distance: 179 - 189: 56.526 distance: 180 - 211: 27.354 distance: 181 - 182: 27.240 distance: 182 - 183: 16.567 distance: 182 - 184: 33.738 distance: 183 - 185: 33.325 distance: 184 - 186: 25.097 distance: 185 - 187: 18.728 distance: 186 - 187: 25.819 distance: 187 - 188: 25.611 distance: 189 - 190: 57.194 distance: 190 - 191: 36.234 distance: 190 - 193: 45.715 distance: 191 - 192: 27.952 distance: 191 - 197: 30.188 distance: 192 - 219: 32.283 distance: 193 - 194: 5.605 distance: 194 - 195: 53.953 distance: 194 - 196: 44.532