Starting phenix.real_space_refine on Wed Jun 3 15:36:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z3j_73786/06_2026/9z3j_73786.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z3j_73786/06_2026/9z3j_73786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z3j_73786/06_2026/9z3j_73786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z3j_73786/06_2026/9z3j_73786.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z3j_73786/06_2026/9z3j_73786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z3j_73786/06_2026/9z3j_73786.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.069 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 38 5.16 5 C 4271 2.51 5 N 1156 2.21 5 O 1308 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-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6773 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 67 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2545 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 3, 'GLN:plan1': 2, 'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "H" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1579 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1598 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 857 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.02, per 1000 atoms: 0.30 Number of scatterers: 6773 At special positions: 0 Unit cell: (71.294, 78.755, 130.982, 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 38 16.00 O 1308 8.00 N 1156 7.00 C 4271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 297 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 447 " distance=2.02 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 465 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS N 25 " - pdb=" SG CYS N 99 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN B 213 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 390.1 milliseconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 18 sheets defined 10.7% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 872 through 877 Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.510A pdb=" N GLY B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.651A pdb=" N GLU B 299 " --> pdb=" O HIS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 480 through 491 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.568A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 192 through 196 Processing helix chain 'H' and resid 208 through 211 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.943A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'N' and resid 65 through 68 Processing helix chain 'N' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'B' and resid 149 through 152 Processing sheet with id=AA2, first strand: chain 'B' and resid 196 through 200 Processing sheet with id=AA3, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AA4, first strand: chain 'B' and resid 260 through 261 removed outlier: 4.263A pdb=" N CYS B 426 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL B 473 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 445 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER B 382 " --> pdb=" O PRO B 444 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER B 448 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 378 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 270 through 275 removed outlier: 6.415A pdb=" N VAL B 275 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N HIS B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 348 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL B 331 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS B 350 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TRP B 308 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.799A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.831A pdb=" N CYS H 96 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TRP H 110 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG H 98 " --> pdb=" O ASP H 108 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR H 106 " --> pdb=" O GLY H 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 127 through 131 removed outlier: 5.181A pdb=" N ALA H 144 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL H 191 " --> pdb=" O ALA H 144 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLY H 146 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL H 189 " --> pdb=" O GLY H 146 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 127 through 131 removed outlier: 5.181A pdb=" N ALA H 144 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL H 191 " --> pdb=" O ALA H 144 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLY H 146 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL H 189 " --> pdb=" O GLY H 146 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 158 through 161 removed outlier: 4.334A pdb=" N TYR H 201 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.772A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.450A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.722A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AB7, first strand: chain 'N' and resid 6 through 10 Processing sheet with id=AB8, first strand: chain 'N' and resid 13 through 14 removed outlier: 6.209A pdb=" N GLY N 13 " --> pdb=" O THR N 121 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA N 36 " --> pdb=" O ASP N 102 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET N 37 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL N 53 " --> pdb=" O MET N 37 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP N 39 " --> pdb=" O VAL N 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 13 through 14 removed outlier: 6.209A pdb=" N GLY N 13 " --> pdb=" O THR N 121 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR N 113 " --> pdb=" O ILE N 101 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 654 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: 1.25 Time building geometry restraints manager: 0.77 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: 2165 1.34 - 1.46: 1667 1.46 - 1.58: 2967 1.58 - 1.70: 0 1.70 - 1.82: 52 Bond restraints: 6851 Sorted by residual: bond pdb=" C TYR L 140 " pdb=" N PRO L 141 " ideal model delta sigma weight residual 1.332 1.347 -0.015 1.12e-02 7.97e+03 1.84e+00 bond pdb=" CA THR B 287 " pdb=" CB THR B 287 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.58e-02 4.01e+03 1.18e+00 bond pdb=" C ALA N 43 " pdb=" N PRO N 44 " ideal model delta sigma weight residual 1.332 1.343 -0.011 1.12e-02 7.97e+03 1.03e+00 bond pdb=" CB VAL N 51 " pdb=" CG2 VAL N 51 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.02e+00 bond pdb=" CA VAL L 58 " pdb=" CB VAL L 58 " ideal model delta sigma weight residual 1.537 1.524 0.013 1.29e-02 6.01e+03 1.01e+00 ... (remaining 6846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 9106 1.68 - 3.36: 213 3.36 - 5.03: 25 5.03 - 6.71: 4 6.71 - 8.39: 1 Bond angle restraints: 9349 Sorted by residual: angle pdb=" N ILE L 29 " pdb=" CA ILE L 29 " pdb=" C ILE L 29 " ideal model delta sigma weight residual 111.88 108.41 3.47 1.06e+00 8.90e-01 1.07e+01 angle pdb=" C TRP H 102 " pdb=" N VAL H 103 " pdb=" CA VAL H 103 " ideal model delta sigma weight residual 121.97 127.00 -5.03 1.80e+00 3.09e-01 7.82e+00 angle pdb=" CA LEU H 185 " pdb=" CB LEU H 185 " pdb=" CG LEU H 185 " ideal model delta sigma weight residual 116.30 124.69 -8.39 3.50e+00 8.16e-02 5.75e+00 angle pdb=" C GLY B 432 " pdb=" N ASN B 433 " pdb=" CA ASN B 433 " ideal model delta sigma weight residual 121.54 125.92 -4.38 1.91e+00 2.74e-01 5.25e+00 angle pdb=" CA CYS B 281 " pdb=" CB CYS B 281 " pdb=" SG CYS B 281 " ideal model delta sigma weight residual 114.40 119.37 -4.97 2.30e+00 1.89e-01 4.66e+00 ... (remaining 9344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 3782 17.55 - 35.09: 180 35.09 - 52.64: 55 52.64 - 70.18: 21 70.18 - 87.73: 6 Dihedral angle restraints: 4044 sinusoidal: 1470 harmonic: 2574 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 5.27 87.73 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS B 281 " pdb=" SG CYS B 281 " pdb=" SG CYS B 297 " pdb=" CB CYS B 297 " ideal model delta sinusoidal sigma weight residual 93.00 150.31 -57.31 1 1.00e+01 1.00e-02 4.42e+01 dihedral pdb=" CB CYS H 147 " pdb=" SG CYS H 147 " pdb=" SG CYS H 203 " pdb=" CB CYS H 203 " ideal model delta sinusoidal sigma weight residual 93.00 55.39 37.61 1 1.00e+01 1.00e-02 2.00e+01 ... (remaining 4041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 529 0.030 - 0.060: 324 0.060 - 0.090: 105 0.090 - 0.120: 69 0.120 - 0.151: 11 Chirality restraints: 1038 Sorted by residual: chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE B 291 " pdb=" N ILE B 291 " pdb=" C ILE B 291 " pdb=" CB ILE B 291 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 1035 not shown) Planarity restraints: 1205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS H 96 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C CYS H 96 " -0.026 2.00e-02 2.50e+03 pdb=" O CYS H 96 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA H 97 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP L 81 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" CG ASP L 81 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP L 81 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP L 81 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 304 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.14e+00 pdb=" N PRO B 305 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 305 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 305 " 0.020 5.00e-02 4.00e+02 ... (remaining 1202 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 910 2.76 - 3.29: 6051 3.29 - 3.83: 11645 3.83 - 4.36: 14579 4.36 - 4.90: 25072 Nonbonded interactions: 58257 Sorted by model distance: nonbonded pdb=" O GLN B 270 " pdb=" O HOH B 601 " model vdw 2.223 3.040 nonbonded pdb=" OE2 GLU L 161 " pdb=" O HOH L 301 " model vdw 2.228 3.040 nonbonded pdb=" OG SER B 272 " pdb=" ND1 HIS B 279 " model vdw 2.231 3.120 nonbonded pdb=" OD1 ASP B 435 " pdb=" O HOH B 602 " model vdw 2.301 3.040 nonbonded pdb=" O VAL B 364 " pdb=" O HOH B 603 " model vdw 2.305 3.040 ... (remaining 58252 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: 11.440 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.820 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:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 0.040 6866 Z= 0.180 Angle : 0.632 8.391 9382 Z= 0.348 Chirality : 0.047 0.151 1038 Planarity : 0.005 0.044 1204 Dihedral : 12.749 86.777 2366 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.27 % Favored : 97.62 % Rotamer: Outliers : 0.32 % Allowed : 7.73 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.93 (0.29), residues: 881 helix: -1.53 (0.63), residues: 54 sheet: 0.89 (0.28), residues: 325 loop : 0.85 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 16 TYR 0.024 0.002 TYR B 485 PHE 0.016 0.002 PHE L 139 TRP 0.020 0.002 TRP H 102 HIS 0.006 0.002 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 6851) covalent geometry : angle 0.62325 / 0.34 ( 9349) SS BOND : bond 0.00413 / 0.26 ( 12) SS BOND : angle 2.09755 / 1.53 ( 24) hydrogen bonds : bond 0.12184 / 7.95 ( 256) hydrogen bonds : angle 7.32579 / 5.12 ( 654) link_BETA1-4 : bond 0.00371 / 0.20 ( 1) link_BETA1-4 : angle 1.23779 / 0.54 ( 3) link_BETA1-6 : bond 0.00388 / 0.20 ( 1) link_BETA1-6 : angle 1.27823 / 0.64 ( 3) link_NAG-ASN : bond 0.00092 / 0.05 ( 1) link_NAG-ASN : angle 1.11424 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.266 Fit side-chains REVERT: H 65 LYS cc_start: 0.8327 (ttmt) cc_final: 0.8037 (ttmm) outliers start: 2 outliers final: 1 residues processed: 89 average time/residue: 0.7493 time to fit residues: 69.5109 Evaluate side-chains 74 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 212 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 HIS B 327 GLN B 451 ASN H 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.119512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097551 restraints weight = 7571.310| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.43 r_work: 0.2836 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 6866 Z= 0.194 Angle : 0.589 8.646 9382 Z= 0.313 Chirality : 0.046 0.153 1038 Planarity : 0.005 0.036 1204 Dihedral : 4.706 18.977 1026 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.42 % Allowed : 6.47 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.85 (0.29), residues: 881 helix: -1.27 (0.65), residues: 56 sheet: 0.90 (0.28), residues: 312 loop : 0.72 (0.30), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 16 TYR 0.013 0.002 TYR B 485 PHE 0.015 0.002 PHE H 107 TRP 0.013 0.002 TRP B 306 HIS 0.005 0.002 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 ( 6851) covalent geometry : angle 0.58522 / 0.31 ( 9349) SS BOND : bond 0.00298 / 0.17 ( 12) SS BOND : angle 1.29852 / 0.89 ( 24) hydrogen bonds : bond 0.03713 / 2.59 ( 256) hydrogen bonds : angle 6.30860 / 4.45 ( 654) link_BETA1-4 : bond 0.00353 / 0.19 ( 1) link_BETA1-4 : angle 1.54183 / 0.67 ( 3) link_BETA1-6 : bond 0.00332 / 0.17 ( 1) link_BETA1-6 : angle 1.28423 / 0.65 ( 3) link_NAG-ASN : bond 0.00104 / 0.05 ( 1) link_NAG-ASN : angle 1.15346 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.259 Fit side-chains REVERT: B 289 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8016 (mt-10) REVERT: B 424 MET cc_start: 0.8944 (mtt) cc_final: 0.8726 (mtt) REVERT: H 65 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8241 (ttmm) REVERT: H 199 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.6550 (tm-30) REVERT: L 105 GLU cc_start: 0.8929 (pt0) cc_final: 0.8702 (pt0) REVERT: N 68 GLN cc_start: 0.8474 (tp40) cc_final: 0.8236 (tp-100) outliers start: 9 outliers final: 5 residues processed: 87 average time/residue: 0.6897 time to fit residues: 62.6568 Evaluate side-chains 82 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 316 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 52 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 72 optimal weight: 0.0050 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 HIS H 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.120904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.100162 restraints weight = 7488.104| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.32 r_work: 0.2917 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6866 Z= 0.141 Angle : 0.528 8.040 9382 Z= 0.280 Chirality : 0.044 0.144 1038 Planarity : 0.004 0.035 1204 Dihedral : 4.459 18.145 1026 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.42 % Allowed : 7.73 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.86 (0.29), residues: 881 helix: -0.98 (0.68), residues: 56 sheet: 0.90 (0.28), residues: 318 loop : 0.69 (0.30), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 16 TYR 0.011 0.001 TYR L 91 PHE 0.012 0.001 PHE N 50 TRP 0.012 0.001 TRP B 306 HIS 0.005 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 6851) covalent geometry : angle 0.52544 / 0.28 ( 9349) SS BOND : bond 0.00223 / 0.13 ( 12) SS BOND : angle 0.99355 / 0.63 ( 24) hydrogen bonds : bond 0.03309 / 2.29 ( 256) hydrogen bonds : angle 5.92902 / 4.16 ( 654) link_BETA1-4 : bond 0.00434 / 0.23 ( 1) link_BETA1-4 : angle 1.47502 / 0.64 ( 3) link_BETA1-6 : bond 0.00277 / 0.15 ( 1) link_BETA1-6 : angle 1.20040 / 0.60 ( 3) link_NAG-ASN : bond 0.00029 / 0.02 ( 1) link_NAG-ASN : angle 1.06471 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.185 Fit side-chains REVERT: B 289 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8086 (mt-10) REVERT: B 409 ARG cc_start: 0.7654 (tpt170) cc_final: 0.7392 (tpt170) REVERT: H 65 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8239 (ttmm) REVERT: H 199 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.6677 (tm-30) outliers start: 9 outliers final: 6 residues processed: 86 average time/residue: 0.6359 time to fit residues: 57.2359 Evaluate side-chains 81 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 316 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN N 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.103275 restraints weight = 7114.716| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.47 r_work: 0.2971 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 6866 Z= 0.209 Angle : 0.588 8.277 9382 Z= 0.308 Chirality : 0.046 0.155 1038 Planarity : 0.005 0.040 1204 Dihedral : 4.695 19.719 1026 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.74 % Allowed : 8.68 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.65 (0.29), residues: 881 helix: -1.15 (0.66), residues: 56 sheet: 0.77 (0.28), residues: 318 loop : 0.54 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 186 TYR 0.012 0.002 TYR L 86 PHE 0.014 0.002 PHE N 50 TRP 0.011 0.001 TRP B 306 HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 ( 6851) covalent geometry : angle 0.58446 / 0.31 ( 9349) SS BOND : bond 0.00245 / 0.16 ( 12) SS BOND : angle 1.20136 / 0.79 ( 24) hydrogen bonds : bond 0.03491 / 2.44 ( 256) hydrogen bonds : angle 6.10191 / 4.27 ( 654) link_BETA1-4 : bond 0.00425 / 0.22 ( 1) link_BETA1-4 : angle 1.72881 / 0.74 ( 3) link_BETA1-6 : bond 0.00220 / 0.12 ( 1) link_BETA1-6 : angle 1.27669 / 0.66 ( 3) link_NAG-ASN : bond 0.00139 / 0.07 ( 1) link_NAG-ASN : angle 1.30144 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.200 Fit side-chains REVERT: B 203 ASP cc_start: 0.7559 (m-30) cc_final: 0.7209 (m-30) REVERT: B 409 ARG cc_start: 0.7693 (tpt170) cc_final: 0.6998 (ttp-110) REVERT: H 199 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.6555 (tm-30) outliers start: 11 outliers final: 6 residues processed: 81 average time/residue: 0.6947 time to fit residues: 58.6170 Evaluate side-chains 78 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN N 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.127466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.105998 restraints weight = 7077.122| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.39 r_work: 0.2975 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6866 Z= 0.180 Angle : 0.560 8.267 9382 Z= 0.293 Chirality : 0.045 0.146 1038 Planarity : 0.004 0.036 1204 Dihedral : 4.601 19.611 1026 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.89 % Allowed : 9.94 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.68 (0.28), residues: 881 helix: -1.12 (0.66), residues: 56 sheet: 0.79 (0.28), residues: 319 loop : 0.55 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 186 TYR 0.011 0.002 TYR L 91 PHE 0.012 0.002 PHE N 50 TRP 0.010 0.001 TRP B 306 HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 6851) covalent geometry : angle 0.55680 / 0.29 ( 9349) SS BOND : bond 0.00223 / 0.13 ( 12) SS BOND : angle 1.07231 / 0.67 ( 24) hydrogen bonds : bond 0.03278 / 2.29 ( 256) hydrogen bonds : angle 5.98546 / 4.18 ( 654) link_BETA1-4 : bond 0.00393 / 0.21 ( 1) link_BETA1-4 : angle 1.60773 / 0.69 ( 3) link_BETA1-6 : bond 0.00269 / 0.14 ( 1) link_BETA1-6 : angle 1.23467 / 0.63 ( 3) link_NAG-ASN : bond 0.00116 / 0.06 ( 1) link_NAG-ASN : angle 1.33091 / 0.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.301 Fit side-chains REVERT: B 203 ASP cc_start: 0.7476 (m-30) cc_final: 0.7163 (m-30) REVERT: B 409 ARG cc_start: 0.7769 (tpt170) cc_final: 0.7142 (ttp-110) REVERT: H 43 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7951 (mtmt) outliers start: 12 outliers final: 8 residues processed: 82 average time/residue: 0.6896 time to fit residues: 59.1702 Evaluate side-chains 76 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 72 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 chunk 66 optimal weight: 0.0870 chunk 38 optimal weight: 0.8980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 ASN H 77 ASN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.130131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.108602 restraints weight = 7089.233| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.41 r_work: 0.3019 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6866 Z= 0.111 Angle : 0.501 7.565 9382 Z= 0.263 Chirality : 0.043 0.137 1038 Planarity : 0.004 0.035 1204 Dihedral : 4.304 18.226 1025 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.05 % Allowed : 9.46 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.82 (0.29), residues: 881 helix: -0.90 (0.68), residues: 56 sheet: 0.92 (0.28), residues: 316 loop : 0.62 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 16 TYR 0.011 0.001 TYR L 91 PHE 0.008 0.001 PHE H 107 TRP 0.012 0.001 TRP B 306 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 6851) covalent geometry : angle 0.49793 / 0.26 ( 9349) SS BOND : bond 0.00179 / 0.10 ( 12) SS BOND : angle 0.85239 / 0.50 ( 24) hydrogen bonds : bond 0.02859 / 1.99 ( 256) hydrogen bonds : angle 5.59989 / 3.93 ( 654) link_BETA1-4 : bond 0.00421 / 0.22 ( 1) link_BETA1-4 : angle 1.44171 / 0.61 ( 3) link_BETA1-6 : bond 0.00421 / 0.22 ( 1) link_BETA1-6 : angle 1.22438 / 0.60 ( 3) link_NAG-ASN : bond 0.00022 / 0.01 ( 1) link_NAG-ASN : angle 1.19309 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.317 Fit side-chains REVERT: B 203 ASP cc_start: 0.7471 (m-30) cc_final: 0.7196 (m-30) REVERT: B 409 ARG cc_start: 0.7737 (tpt170) cc_final: 0.7145 (ttp-110) REVERT: H 196 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7603 (mp) outliers start: 13 outliers final: 7 residues processed: 84 average time/residue: 0.6655 time to fit residues: 58.5480 Evaluate side-chains 77 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 76 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 4 optimal weight: 0.0570 chunk 86 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN N 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.127779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.105767 restraints weight = 7042.261| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.46 r_work: 0.2991 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6866 Z= 0.144 Angle : 0.528 7.744 9382 Z= 0.275 Chirality : 0.044 0.140 1038 Planarity : 0.004 0.035 1204 Dihedral : 4.354 18.864 1025 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.89 % Allowed : 9.62 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.78 (0.29), residues: 881 helix: -0.99 (0.67), residues: 56 sheet: 0.92 (0.28), residues: 312 loop : 0.58 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 316 TYR 0.011 0.001 TYR L 91 PHE 0.011 0.001 PHE L 98 TRP 0.019 0.001 TRP B 306 HIS 0.003 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 6851) covalent geometry : angle 0.52461 / 0.27 ( 9349) SS BOND : bond 0.00183 / 0.11 ( 12) SS BOND : angle 0.96167 / 0.59 ( 24) hydrogen bonds : bond 0.02993 / 2.09 ( 256) hydrogen bonds : angle 5.64970 / 3.96 ( 654) link_BETA1-4 : bond 0.00388 / 0.20 ( 1) link_BETA1-4 : angle 1.57271 / 0.66 ( 3) link_BETA1-6 : bond 0.00345 / 0.18 ( 1) link_BETA1-6 : angle 1.23431 / 0.61 ( 3) link_NAG-ASN : bond 0.00065 / 0.03 ( 1) link_NAG-ASN : angle 1.29621 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.264 Fit side-chains REVERT: B 203 ASP cc_start: 0.7452 (m-30) cc_final: 0.7167 (m-30) REVERT: B 409 ARG cc_start: 0.7686 (tpt170) cc_final: 0.7036 (ttp-110) REVERT: H 43 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7836 (mtmt) REVERT: H 196 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7534 (mp) REVERT: H 199 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.6720 (tm-30) REVERT: N 42 GLN cc_start: 0.8357 (tp40) cc_final: 0.8150 (tp-100) outliers start: 12 outliers final: 9 residues processed: 80 average time/residue: 0.6929 time to fit residues: 57.9679 Evaluate side-chains 81 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/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-dev-6079/lib/python3.9/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/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-dev-6079/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-dev-6079/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-dev-6079/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-dev-6079/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-dev-6079/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-dev-6079/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-dev-6079/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-dev-6079/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-dev-6079/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-dev-6079/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-dev-6079/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-dev-6079/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-dev-6079/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-dev-6079/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-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.8828 > 50: distance: 11 - 13: 7.546 distance: 13 - 14: 7.983 distance: 14 - 15: 6.859 distance: 14 - 17: 10.171 distance: 15 - 16: 12.272 distance: 15 - 18: 6.395 distance: 18 - 19: 5.264 distance: 19 - 20: 9.564 distance: 20 - 21: 19.338 distance: 20 - 25: 33.632 distance: 22 - 23: 13.649 distance: 22 - 24: 20.163 distance: 25 - 26: 29.948 distance: 26 - 27: 19.731 distance: 26 - 29: 14.439 distance: 27 - 28: 10.939 distance: 27 - 34: 34.575 distance: 29 - 30: 33.819 distance: 30 - 31: 11.215 distance: 31 - 32: 22.049 distance: 31 - 33: 16.382 distance: 34 - 35: 11.199 distance: 34 - 40: 14.545 distance: 35 - 36: 12.924 distance: 35 - 38: 21.424 distance: 36 - 37: 15.661 distance: 36 - 41: 14.459 distance: 38 - 39: 19.538 distance: 39 - 40: 29.786 distance: 41 - 42: 23.606 distance: 42 - 43: 12.919 distance: 43 - 44: 13.904 distance: 43 - 45: 21.650 distance: 45 - 46: 22.654 distance: 46 - 47: 18.438 distance: 47 - 48: 27.513 distance: 47 - 49: 17.731 distance: 49 - 50: 23.694 distance: 50 - 51: 20.994 distance: 50 - 53: 23.113 distance: 51 - 52: 23.758 distance: 51 - 54: 16.349 distance: 54 - 55: 35.231 distance: 54 - 124: 24.923 distance: 55 - 56: 34.176 distance: 55 - 58: 34.425 distance: 56 - 57: 30.576 distance: 56 - 62: 27.922 distance: 57 - 121: 32.823 distance: 58 - 59: 27.523 distance: 59 - 60: 20.785 distance: 59 - 61: 30.765 distance: 62 - 63: 28.162 distance: 63 - 64: 14.666 distance: 63 - 66: 10.100 distance: 64 - 65: 5.262 distance: 64 - 73: 31.559 distance: 66 - 67: 13.276 distance: 67 - 68: 15.868 distance: 68 - 69: 8.417 distance: 69 - 70: 3.657 distance: 70 - 71: 4.726 distance: 73 - 74: 28.165 distance: 73 - 108: 17.919 distance: 74 - 75: 34.828 distance: 74 - 77: 12.679 distance: 75 - 76: 16.583 distance: 75 - 81: 11.570 distance: 76 - 105: 29.756 distance: 77 - 78: 37.557 distance: 78 - 79: 29.010 distance: 78 - 80: 35.546