Starting phenix.real_space_refine on Thu Feb 5 06:28:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hjm_52218/02_2026/9hjm_52218.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hjm_52218/02_2026/9hjm_52218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hjm_52218/02_2026/9hjm_52218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hjm_52218/02_2026/9hjm_52218.map" model { file = "/net/cci-nas-00/data/ceres_data/9hjm_52218/02_2026/9hjm_52218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hjm_52218/02_2026/9hjm_52218.cif" } resolution = 3.24 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= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 9797 2.51 5 N 2555 2.21 5 O 2883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 15297 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3102 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 15, 'TRANS': 377} Chain breaks: 1 Chain: "G" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3454 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 24, 'TRANS': 414} Chain: "H" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3268 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 18, 'TRANS': 398} Chain: "I" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1218 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "J" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1418 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain: "A" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'PLM': 1, 'Z41': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.23, per 1000 atoms: 0.21 Number of scatterers: 15297 At special positions: 0 Unit cell: (102.48, 104.16, 187.32, 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 62 16.00 O 2883 8.00 N 2555 7.00 C 9797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 550.3 milliseconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3530 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 23 sheets defined 9.5% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'F' and resid 38 through 43 Processing helix chain 'F' and resid 53 through 59 Processing helix chain 'F' and resid 76 through 81 removed outlier: 3.725A pdb=" N SER F 81 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 186 removed outlier: 4.541A pdb=" N GLY G 177 " --> pdb=" O PRO G 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 185 " --> pdb=" O TYR G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 201 Processing helix chain 'G' and resid 261 through 266 removed outlier: 3.624A pdb=" N LEU G 265 " --> pdb=" O ILE G 261 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN G 266 " --> pdb=" O SER G 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 261 through 266' Processing helix chain 'G' and resid 287 through 293 removed outlier: 3.757A pdb=" N PHE G 291 " --> pdb=" O SER G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 345 removed outlier: 3.821A pdb=" N PHE G 343 " --> pdb=" O VAL G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 384 removed outlier: 3.538A pdb=" N LEU G 378 " --> pdb=" O ILE G 374 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 removed outlier: 4.111A pdb=" N LEU H 56 " --> pdb=" O ASN H 53 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU H 57 " --> pdb=" O PRO H 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 57' Processing helix chain 'H' and resid 284 through 287 Processing helix chain 'H' and resid 399 through 404 Processing helix chain 'H' and resid 407 through 411 Processing helix chain 'I' and resid 32 through 49 removed outlier: 3.772A pdb=" N ALA I 47 " --> pdb=" O PHE I 43 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP I 48 " --> pdb=" O ASN I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 130 Processing helix chain 'I' and resid 143 through 148 Processing helix chain 'J' and resid 33 through 48 removed outlier: 3.662A pdb=" N ASN J 48 " --> pdb=" O GLU J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 155 removed outlier: 3.556A pdb=" N VAL J 155 " --> pdb=" O ASP J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 161 Processing helix chain 'J' and resid 162 through 165 Processing helix chain 'J' and resid 177 through 181 Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 703 through 708 Processing helix chain 'A' and resid 792 through 796 Processing helix chain 'A' and resid 834 through 838 Processing sheet with id=AA1, first strand: chain 'F' and resid 47 through 48 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 47 through 48 current: chain 'F' and resid 107 through 114 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 107 through 114 current: chain 'F' and resid 129 through 149 removed outlier: 5.507A pdb=" N MET F 130 " --> pdb=" O GLY F 175 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY F 175 " --> pdb=" O MET F 130 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ALA F 132 " --> pdb=" O GLY F 173 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY F 173 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL F 134 " --> pdb=" O TYR F 171 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR F 171 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASP F 169 " --> pdb=" O PRO F 136 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE F 192 " --> pdb=" O ASN F 168 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 191 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 201 " --> pdb=" O PRO F 211 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 238 through 247 current: chain 'F' and resid 272 through 285 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 272 through 285 current: chain 'F' and resid 301 through 310 removed outlier: 4.559A pdb=" N ILE F 328 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU F 412 " --> pdb=" O LEU F 403 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 323 through 324 Processing sheet with id=AA3, first strand: chain 'G' and resid 39 through 45 removed outlier: 6.430A pdb=" N MET G 450 " --> pdb=" O ILE G 307 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE G 307 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR G 452 " --> pdb=" O TRP G 305 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TRP G 305 " --> pdb=" O TYR G 452 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 47 through 52 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 280 through 286 current: chain 'G' and resid 357 through 358 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 357 through 358 current: chain 'G' and resid 419 through 425 Processing sheet with id=AA5, first strand: chain 'G' and resid 63 through 70 removed outlier: 8.862A pdb=" N LEU G 64 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR G 80 " --> pdb=" O LEU G 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 74 through 82 current: chain 'G' and resid 151 through 158 Processing sheet with id=AA6, first strand: chain 'G' and resid 227 through 228 Processing sheet with id=AA7, first strand: chain 'G' and resid 272 through 275 Processing sheet with id=AA8, first strand: chain 'G' and resid 313 through 315 Processing sheet with id=AA9, first strand: chain 'G' and resid 386 through 389 removed outlier: 3.621A pdb=" N THR G 389 " --> pdb=" O LYS G 393 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS G 393 " --> pdb=" O THR G 389 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 43 through 50 removed outlier: 3.518A pdb=" N ARG H 45 " --> pdb=" O VAL H 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 62 through 64 removed outlier: 4.536A pdb=" N LEU H 98 " --> pdb=" O TRP H 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 153 through 158 removed outlier: 4.750A pdb=" N ILE H 445 " --> pdb=" O LEU H 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 172 through 176 Processing sheet with id=AB5, first strand: chain 'H' and resid 217 through 220 Processing sheet with id=AB6, first strand: chain 'H' and resid 252 through 258 removed outlier: 7.479A pdb=" N VAL H 252 " --> pdb=" O GLU H 273 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU H 273 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA H 269 " --> pdb=" O LEU H 256 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU H 292 " --> pdb=" O PHE H 280 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR H 282 " --> pdb=" O TRP H 290 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TRP H 290 " --> pdb=" O THR H 282 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 299 through 301 removed outlier: 6.665A pdb=" N VAL H 322 " --> pdb=" O VAL H 300 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 304 through 310 Processing sheet with id=AB9, first strand: chain 'H' and resid 359 through 363 Processing sheet with id=AC1, first strand: chain 'I' and resid 53 through 55 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 64 through 66 current: chain 'I' and resid 98 through 101 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 98 through 101 current: chain 'I' and resid 169 through 178 Processing sheet with id=AC2, first strand: chain 'J' and resid 54 through 56 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 77 through 82 current: chain 'J' and resid 112 through 115 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 112 through 115 current: chain 'J' and resid 137 through 143 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 137 through 143 current: chain 'J' and resid 191 through 201 Processing sheet with id=AC3, first strand: chain 'A' and resid 506 through 507 Processing sheet with id=AC4, first strand: chain 'A' and resid 514 through 518 removed outlier: 3.554A pdb=" N SER A 663 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 676 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS A 714 " --> pdb=" O GLY A 748 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N TYR A 801 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TRP A 832 " --> pdb=" O TYR A 801 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ARG A 803 " --> pdb=" O ASN A 830 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASN A 830 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N THR A 805 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA A 828 " --> pdb=" O THR A 805 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLU A 807 " --> pdb=" O ALA A 826 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA A 826 " --> pdb=" O GLU A 807 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ARG A 809 " --> pdb=" O ALA A 824 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA A 824 " --> pdb=" O ARG A 809 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU A 822 " --> pdb=" O PRO A 811 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 819 " --> pdb=" O THR A 854 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 761 through 763 450 hydrogen bonds defined for protein. 1170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2480 1.31 - 1.44: 4508 1.44 - 1.57: 8579 1.57 - 1.70: 1 1.70 - 1.83: 115 Bond restraints: 15683 Sorted by residual: bond pdb=" CG LEU I 93 " pdb=" CD2 LEU I 93 " ideal model delta sigma weight residual 1.521 1.308 0.213 3.30e-02 9.18e+02 4.17e+01 bond pdb=" CD2 TYR I 46 " pdb=" CE2 TYR I 46 " ideal model delta sigma weight residual 1.382 1.247 0.135 3.00e-02 1.11e+03 2.03e+01 bond pdb=" CG ASN F 388 " pdb=" ND2 ASN F 388 " ideal model delta sigma weight residual 1.328 1.247 0.081 2.10e-02 2.27e+03 1.50e+01 bond pdb=" CG TYR I 46 " pdb=" CD2 TYR I 46 " ideal model delta sigma weight residual 1.389 1.310 0.079 2.10e-02 2.27e+03 1.41e+01 bond pdb=" C16 Z41 G 502 " pdb=" O2 Z41 G 502 " ideal model delta sigma weight residual 1.332 1.405 -0.073 2.00e-02 2.50e+03 1.32e+01 ... (remaining 15678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 21145 4.15 - 8.31: 77 8.31 - 12.46: 9 12.46 - 16.62: 0 16.62 - 20.77: 1 Bond angle restraints: 21232 Sorted by residual: angle pdb=" CB MET H 127 " pdb=" CG MET H 127 " pdb=" SD MET H 127 " ideal model delta sigma weight residual 112.70 91.93 20.77 3.00e+00 1.11e-01 4.79e+01 angle pdb=" CA MET H 127 " pdb=" CB MET H 127 " pdb=" CG MET H 127 " ideal model delta sigma weight residual 114.10 124.83 -10.73 2.00e+00 2.50e-01 2.88e+01 angle pdb=" C MET F 280 " pdb=" N ASP F 281 " pdb=" CA ASP F 281 " ideal model delta sigma weight residual 122.61 129.73 -7.12 1.56e+00 4.11e-01 2.09e+01 angle pdb=" CB GLU J 39 " pdb=" CG GLU J 39 " pdb=" CD GLU J 39 " ideal model delta sigma weight residual 112.60 105.41 7.19 1.70e+00 3.46e-01 1.79e+01 angle pdb=" CG MET H 127 " pdb=" SD MET H 127 " pdb=" CE MET H 127 " ideal model delta sigma weight residual 100.90 110.06 -9.16 2.20e+00 2.07e-01 1.73e+01 ... (remaining 21227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8636 17.94 - 35.88: 507 35.88 - 53.82: 94 53.82 - 71.76: 11 71.76 - 89.71: 7 Dihedral angle restraints: 9255 sinusoidal: 3699 harmonic: 5556 Sorted by residual: dihedral pdb=" CA TYR G 230 " pdb=" C TYR G 230 " pdb=" N LYS G 231 " pdb=" CA LYS G 231 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ASN F 265 " pdb=" C ASN F 265 " pdb=" N GLY F 266 " pdb=" CA GLY F 266 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR F 117 " pdb=" C TYR F 117 " pdb=" N PHE F 118 " pdb=" CA PHE F 118 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 9252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 2253 0.178 - 0.356: 12 0.356 - 0.534: 0 0.534 - 0.712: 0 0.712 - 0.890: 1 Chirality restraints: 2266 Sorted by residual: chirality pdb=" CG LEU I 93 " pdb=" CB LEU I 93 " pdb=" CD1 LEU I 93 " pdb=" CD2 LEU I 93 " both_signs ideal model delta sigma weight residual False -2.59 -1.70 -0.89 2.00e-01 2.50e+01 1.98e+01 chirality pdb=" CB ILE A 504 " pdb=" CA ILE A 504 " pdb=" CG1 ILE A 504 " pdb=" CG2 ILE A 504 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CG LEU J 90 " pdb=" CB LEU J 90 " pdb=" CD1 LEU J 90 " pdb=" CD2 LEU J 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.90 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 2263 not shown) Planarity restraints: 2725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 645 " -0.009 2.00e-02 2.50e+03 3.81e-02 2.54e+01 pdb=" CG PHE A 645 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE A 645 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 PHE A 645 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE A 645 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 PHE A 645 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 645 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 52 " 0.035 2.00e-02 2.50e+03 3.20e-02 1.79e+01 pdb=" CG PHE I 52 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE I 52 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE I 52 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE I 52 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE I 52 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE I 52 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 845 " 0.351 9.50e-02 1.11e+02 1.57e-01 1.52e+01 pdb=" NE ARG A 845 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 845 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 845 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 845 " 0.011 2.00e-02 2.50e+03 ... (remaining 2722 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 83 2.51 - 3.11: 11046 3.11 - 3.71: 21760 3.71 - 4.30: 31749 4.30 - 4.90: 54825 Nonbonded interactions: 119463 Sorted by model distance: nonbonded pdb=" OE1 GLU J 39 " pdb=" OG1 THR J 191 " model vdw 1.915 3.040 nonbonded pdb=" OE2 GLU F 103 " pdb=" OG SER G 29 " model vdw 2.145 3.040 nonbonded pdb=" O SER G 236 " pdb=" OG1 THR G 237 " model vdw 2.175 3.040 nonbonded pdb=" OG SER F 95 " pdb=" OE2 GLU F 116 " model vdw 2.249 3.040 nonbonded pdb=" O VAL J 159 " pdb=" OH TYR J 199 " model vdw 2.253 3.040 ... (remaining 119458 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: 3.690 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: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 13.240 Find NCS groups from input model: 0.080 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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 0.213 15685 Z= 0.223 Angle : 0.798 20.771 21232 Z= 0.418 Chirality : 0.054 0.890 2266 Planarity : 0.007 0.157 2725 Dihedral : 11.984 89.706 5725 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.04 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % 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: -1.33 (0.19), residues: 1902 helix: -0.67 (0.44), residues: 134 sheet: 0.06 (0.18), residues: 844 loop : -1.85 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 45 TYR 0.034 0.002 TYR H 148 PHE 0.072 0.003 PHE A 645 TRP 0.035 0.002 TRP A 534 HIS 0.011 0.001 HIS H 122 Details of bonding type rmsd covalent geometry : bond 0.00474 (15683) covalent geometry : angle 0.79823 (21232) hydrogen bonds : bond 0.13959 ( 450) hydrogen bonds : angle 6.15176 ( 1170) Misc. bond : bond 0.05710 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: G 229 SER cc_start: 0.7845 (t) cc_final: 0.7379 (m) REVERT: H 86 MET cc_start: 0.6747 (ptm) cc_final: 0.6520 (ptp) REVERT: H 127 MET cc_start: 0.7203 (ttt) cc_final: 0.6832 (tpt) REVERT: H 334 ILE cc_start: 0.8521 (pt) cc_final: 0.8230 (pt) REVERT: I 36 ARG cc_start: 0.7474 (mtm180) cc_final: 0.7154 (mtp180) REVERT: I 85 GLU cc_start: 0.8212 (pm20) cc_final: 0.7850 (pm20) REVERT: I 145 TYR cc_start: 0.7060 (p90) cc_final: 0.6749 (p90) REVERT: J 186 TYR cc_start: 0.8045 (t80) cc_final: 0.7637 (t80) REVERT: A 552 THR cc_start: 0.6485 (m) cc_final: 0.6213 (m) REVERT: A 743 GLU cc_start: 0.8443 (pt0) cc_final: 0.8233 (pt0) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1109 time to fit residues: 31.6410 Evaluate side-chains 153 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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-2.0-5952/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: 62.5266 > 50: distance: 161 - 166: 19.492 distance: 166 - 167: 29.864 distance: 167 - 168: 6.838 distance: 167 - 170: 7.535 distance: 168 - 169: 21.411 distance: 168 - 175: 23.637 distance: 170 - 171: 16.872 distance: 171 - 172: 12.512 distance: 172 - 173: 5.362 distance: 173 - 174: 9.375 distance: 175 - 176: 16.389 distance: 176 - 177: 39.910 distance: 176 - 179: 15.423 distance: 177 - 178: 11.852 distance: 177 - 183: 19.450 distance: 179 - 180: 11.130 distance: 180 - 181: 17.261 distance: 180 - 182: 17.137 distance: 183 - 184: 18.676 distance: 184 - 185: 14.918 distance: 184 - 187: 18.588 distance: 185 - 186: 21.000 distance: 185 - 191: 10.123 distance: 187 - 188: 14.022 distance: 188 - 189: 10.531 distance: 188 - 190: 11.733 distance: 191 - 192: 25.601 distance: 192 - 193: 17.087 distance: 192 - 195: 9.650 distance: 193 - 194: 20.912 distance: 193 - 198: 28.328 distance: 195 - 196: 30.925 distance: 195 - 197: 21.223 distance: 198 - 199: 35.866 distance: 199 - 200: 35.289 distance: 199 - 202: 58.869 distance: 200 - 201: 30.566 distance: 200 - 206: 20.836 distance: 202 - 203: 39.399 distance: 203 - 204: 30.903 distance: 203 - 205: 18.429 distance: 206 - 207: 19.552 distance: 207 - 208: 25.865 distance: 207 - 210: 8.898 distance: 208 - 209: 27.890 distance: 208 - 213: 24.398 distance: 210 - 211: 25.872 distance: 210 - 212: 12.414 distance: 213 - 214: 11.822 distance: 214 - 215: 36.870 distance: 214 - 217: 32.853 distance: 215 - 216: 44.488 distance: 215 - 221: 18.146 distance: 217 - 218: 21.266 distance: 218 - 219: 19.794 distance: 218 - 220: 20.149 distance: 221 - 222: 16.725 distance: 222 - 223: 15.361 distance: 222 - 225: 13.045 distance: 223 - 224: 21.973 distance: 223 - 229: 32.062 distance: 225 - 226: 8.594 distance: 226 - 227: 20.106 distance: 226 - 228: 24.484 distance: 229 - 230: 42.946 distance: 229 - 235: 40.288 distance: 230 - 231: 25.228 distance: 230 - 233: 53.607 distance: 231 - 232: 31.237 distance: 231 - 236: 22.039 distance: 233 - 234: 6.321 distance: 234 - 235: 40.337 distance: 236 - 237: 15.191 distance: 237 - 238: 10.076 distance: 237 - 240: 11.396 distance: 238 - 239: 6.229 distance: 238 - 243: 20.501 distance: 240 - 241: 9.727 distance: 240 - 242: 15.155