Starting phenix.real_space_refine on Fri Aug 22 19:12:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8w_29857/08_2025/8g8w_29857_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8w_29857/08_2025/8g8w_29857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g8w_29857/08_2025/8g8w_29857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8w_29857/08_2025/8g8w_29857.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8w_29857/08_2025/8g8w_29857_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8w_29857/08_2025/8g8w_29857_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 23 5.16 5 C 4165 2.51 5 N 1066 2.21 5 O 1209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6471 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2146 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2814 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 24, 'TRANS': 373} Chain breaks: 5 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 16, 'ASP:plan': 10, 'ARG:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 5, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 169 Chain: "C" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1349 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 3 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 422 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 4, 'GLU:plan': 12, 'ASP:plan': 9, 'ASN:plan1': 7, 'TYR:plan': 3, 'HIS:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 179 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 139 Unusual residues: {'CDL': 3, 'GTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-4': 1, 'CDL:plan-1': 2, 'CDL:plan-2': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 1.43, per 1000 atoms: 0.22 Number of scatterers: 6471 At special positions: 0 Unit cell: (72.24, 92.02, 203.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 8 15.00 O 1209 8.00 N 1066 7.00 C 4165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 98 " 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 ALPHA1-4 " GLC D 1 " - " GLC D 2 " Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 304.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 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: 37 helices and 9 sheets defined 48.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 12 through 31 Processing helix chain 'A' and resid 31 through 43 removed outlier: 4.203A pdb=" N ASP A 35 " --> pdb=" O THR A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 70 removed outlier: 3.549A pdb=" N GLY A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 88 through 105 removed outlier: 4.341A pdb=" N ASP A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 130 Processing helix chain 'A' and resid 131 through 144 removed outlier: 4.109A pdb=" N GLU A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 176 through 205 removed outlier: 3.890A pdb=" N ASN A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 242 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 270 through 298 removed outlier: 4.158A pdb=" N LYS A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.931A pdb=" N ASN B 34 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR B 35 " --> pdb=" O LEU B 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 31 through 35' Processing helix chain 'B' and resid 65 through 68 removed outlier: 4.044A pdb=" N GLU B 68 " --> pdb=" O ASP B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.882A pdb=" N THR B 94 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 153 removed outlier: 3.594A pdb=" N LEU B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 172 Proline residue: B 169 - end of helix Processing helix chain 'B' and resid 185 through 195 removed outlier: 4.219A pdb=" N GLY B 189 " --> pdb=" O HIS B 185 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 211 through 217 Processing helix chain 'B' and resid 274 through 277 Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.740A pdb=" N ILE B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'B' and resid 407 through 418 removed outlier: 3.966A pdb=" N ASP B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS B 418 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 433 removed outlier: 3.650A pdb=" N GLU B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.518A pdb=" N LYS B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.614A pdb=" N PHE B 460 " --> pdb=" O GLN B 456 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B 461 " --> pdb=" O MET B 457 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 35 removed outlier: 3.515A pdb=" N TYR C 35 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 109 through 114 removed outlier: 3.532A pdb=" N TYR C 112 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'C' and resid 167 through 172 removed outlier: 3.594A pdb=" N PHE C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 408 removed outlier: 3.602A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.723A pdb=" N GLY B 13 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET B 37 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 52 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG B 41 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE B 50 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 156 through 159 removed outlier: 6.496A pdb=" N LEU B 128 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLU B 159 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE B 130 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA B 385 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AA5, first strand: chain 'B' and resid 346 through 348 Processing sheet with id=AA6, first strand: chain 'C' and resid 8 through 10 Processing sheet with id=AA7, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.813A pdb=" N GLY C 13 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG C 41 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE C 50 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.813A pdb=" N GLY C 13 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 120 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 162 through 163 removed outlier: 7.536A pdb=" N ILE C 134 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU C 387 " --> pdb=" O ILE C 233 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1017 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: 0.80 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1069 1.32 - 1.45: 1808 1.45 - 1.57: 3699 1.57 - 1.69: 15 1.69 - 1.82: 36 Bond restraints: 6627 Sorted by residual: bond pdb=" OA3 CDL A 402 " pdb=" PA1 CDL A 402 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.64e+00 bond pdb=" OB3 CDL A 404 " pdb=" PB2 CDL A 404 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.51e+00 bond pdb=" OB3 CDL A 403 " pdb=" PB2 CDL A 403 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.35e+00 bond pdb=" OA3 CDL A 404 " pdb=" PA1 CDL A 404 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.26e+00 bond pdb=" OA3 CDL A 403 " pdb=" PA1 CDL A 403 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.03e+00 ... (remaining 6622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 8949 2.52 - 5.04: 101 5.04 - 7.57: 18 7.57 - 10.09: 8 10.09 - 12.61: 3 Bond angle restraints: 9079 Sorted by residual: angle pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sigma weight residual 120.50 133.11 -12.61 3.00e+00 1.11e-01 1.77e+01 angle pdb=" C1' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C3' GTP A 401 " ideal model delta sigma weight residual 111.00 99.26 11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O1B GTP A 401 " pdb=" PB GTP A 401 " pdb=" O2B GTP A 401 " ideal model delta sigma weight residual 109.50 119.63 -10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" CB MET B 442 " pdb=" CG MET B 442 " pdb=" SD MET B 442 " ideal model delta sigma weight residual 112.70 122.34 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" PB GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sigma weight residual 120.50 130.08 -9.58 3.00e+00 1.11e-01 1.02e+01 ... (remaining 9074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 3739 35.44 - 70.89: 115 70.89 - 106.33: 5 106.33 - 141.77: 2 141.77 - 177.22: 2 Dihedral angle restraints: 3863 sinusoidal: 1294 harmonic: 2569 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -78.19 -177.22 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual -68.92 83.42 -152.34 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual 303.79 171.36 132.44 1 2.00e+01 2.50e-03 4.02e+01 ... (remaining 3860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 935 0.070 - 0.140: 100 0.140 - 0.210: 4 0.210 - 0.280: 0 0.280 - 0.350: 4 Chirality restraints: 1043 Sorted by residual: chirality pdb=" C1 GLC D 1 " pdb=" C2 GLC D 1 " pdb=" O1 GLC D 1 " pdb=" O5 GLC D 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.39 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" C3' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C4' GTP A 401 " pdb=" O3' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.78 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA4 CDL A 402 " pdb=" CA3 CDL A 402 " pdb=" CA6 CDL A 402 " pdb=" OA6 CDL A 402 " both_signs ideal model delta sigma weight residual False -2.57 -2.27 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 1040 not shown) Planarity restraints: 1152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 89 " 0.043 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO C 90 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 231 " 0.031 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO C 232 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 232 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 232 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 454 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 455 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 455 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 455 " 0.020 5.00e-02 4.00e+02 ... (remaining 1149 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1151 2.77 - 3.30: 5841 3.30 - 3.83: 10176 3.83 - 4.37: 10576 4.37 - 4.90: 19789 Nonbonded interactions: 47533 Sorted by model distance: nonbonded pdb=" OG SER C 55 " pdb=" OH TYR C 112 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASP B 179 " pdb=" OG SER B 391 " model vdw 2.238 3.040 nonbonded pdb=" NE2 GLN A 42 " pdb=" OD2 ASP A 234 " model vdw 2.309 3.120 nonbonded pdb=" O ASP C 75 " pdb=" N ASN C 79 " model vdw 2.316 3.120 nonbonded pdb=" NZ LYS A 138 " pdb=" O1B GTP A 401 " model vdw 2.324 3.120 ... (remaining 47528 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.380 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 0.048 6630 Z= 0.192 Angle : 0.686 12.609 9086 Z= 0.315 Chirality : 0.046 0.350 1043 Planarity : 0.004 0.066 1152 Dihedral : 17.422 177.216 2215 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.18 % Allowed : 19.37 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.29), residues: 880 helix: 2.73 (0.28), residues: 344 sheet: 0.79 (0.40), residues: 144 loop : -0.10 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.011 0.001 TYR C 82 PHE 0.008 0.001 PHE A 286 TRP 0.010 0.001 TRP A 281 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6627) covalent geometry : angle 0.68568 ( 9079) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.29089 ( 4) hydrogen bonds : bond 0.13923 ( 363) hydrogen bonds : angle 5.42106 ( 1017) link_ALPHA1-4 : bond 0.00106 ( 1) link_ALPHA1-4 : angle 0.83297 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.228 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.0583 time to fit residues: 4.5941 Evaluate side-chains 50 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 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: 0.0670 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.157394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.140150 restraints weight = 10785.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.138088 restraints weight = 14578.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.138620 restraints weight = 14562.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138571 restraints weight = 12388.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138606 restraints weight = 11650.462| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6630 Z= 0.136 Angle : 0.524 7.803 9086 Z= 0.262 Chirality : 0.042 0.172 1043 Planarity : 0.004 0.055 1152 Dihedral : 14.009 177.833 1094 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.48 % Allowed : 18.45 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.29), residues: 880 helix: 2.69 (0.28), residues: 361 sheet: 0.83 (0.40), residues: 143 loop : -0.09 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.008 0.001 TYR B 227 PHE 0.007 0.001 PHE B 182 TRP 0.005 0.001 TRP A 281 HIS 0.002 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6627) covalent geometry : angle 0.52380 ( 9079) SS BOND : bond 0.00269 ( 2) SS BOND : angle 0.26259 ( 4) hydrogen bonds : bond 0.04687 ( 363) hydrogen bonds : angle 4.58224 ( 1017) link_ALPHA1-4 : bond 0.00125 ( 1) link_ALPHA1-4 : angle 1.26987 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.158 Fit side-chains REVERT: A 292 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8564 (tt) REVERT: B 41 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8821 (ptp-170) REVERT: B 106 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.7355 (t80) outliers start: 8 outliers final: 3 residues processed: 59 average time/residue: 0.0509 time to fit residues: 4.3348 Evaluate side-chains 53 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 106 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN B 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.151926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141178 restraints weight = 10701.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 85)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.137368 restraints weight = 17113.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.136782 restraints weight = 21424.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.136765 restraints weight = 17878.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.136946 restraints weight = 15736.656| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6630 Z= 0.174 Angle : 0.558 6.535 9086 Z= 0.282 Chirality : 0.043 0.171 1043 Planarity : 0.005 0.056 1152 Dihedral : 13.257 176.406 1094 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.69 % Allowed : 16.79 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.28), residues: 880 helix: 2.52 (0.27), residues: 359 sheet: 0.73 (0.40), residues: 143 loop : -0.17 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 22 TYR 0.010 0.001 TYR C 97 PHE 0.013 0.001 PHE A 224 TRP 0.005 0.001 TRP A 281 HIS 0.003 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 6627) covalent geometry : angle 0.55747 ( 9079) SS BOND : bond 0.00368 ( 2) SS BOND : angle 0.39193 ( 4) hydrogen bonds : bond 0.05188 ( 363) hydrogen bonds : angle 4.56755 ( 1017) link_ALPHA1-4 : bond 0.00063 ( 1) link_ALPHA1-4 : angle 1.30343 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.242 Fit side-chains REVERT: A 155 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8632 (m) REVERT: B 106 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7355 (t80) outliers start: 20 outliers final: 10 residues processed: 68 average time/residue: 0.0529 time to fit residues: 5.3445 Evaluate side-chains 62 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 82 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.152386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.144068 restraints weight = 10709.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.140388 restraints weight = 14661.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138446 restraints weight = 21066.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.138735 restraints weight = 19488.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.138938 restraints weight = 13759.052| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6630 Z= 0.152 Angle : 0.539 6.561 9086 Z= 0.269 Chirality : 0.042 0.167 1043 Planarity : 0.004 0.052 1152 Dihedral : 13.110 178.759 1094 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.77 % Allowed : 18.45 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.28), residues: 880 helix: 2.54 (0.27), residues: 358 sheet: 0.66 (0.40), residues: 143 loop : -0.17 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.009 0.001 TYR B 98 PHE 0.009 0.001 PHE A 224 TRP 0.005 0.001 TRP A 281 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 6627) covalent geometry : angle 0.53871 ( 9079) SS BOND : bond 0.00339 ( 2) SS BOND : angle 0.28345 ( 4) hydrogen bonds : bond 0.04753 ( 363) hydrogen bonds : angle 4.46925 ( 1017) link_ALPHA1-4 : bond 0.00102 ( 1) link_ALPHA1-4 : angle 1.42058 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 155 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8706 (m) REVERT: A 168 GLU cc_start: 0.7826 (tp30) cc_final: 0.7594 (tp30) REVERT: B 30 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7422 (pp) REVERT: C 10 SER cc_start: 0.6379 (m) cc_final: 0.5994 (t) outliers start: 15 outliers final: 10 residues processed: 65 average time/residue: 0.0600 time to fit residues: 5.7404 Evaluate side-chains 62 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.489 > 50: distance: 5 - 105: 34.881 distance: 32 - 39: 35.332 distance: 40 - 41: 38.990 distance: 40 - 43: 40.823 distance: 41 - 42: 40.630 distance: 41 - 44: 39.815 distance: 44 - 45: 46.609 distance: 44 - 50: 56.942 distance: 45 - 46: 40.170 distance: 45 - 48: 41.808 distance: 46 - 47: 42.858 distance: 46 - 51: 22.121 distance: 48 - 49: 14.424 distance: 49 - 50: 56.353 distance: 51 - 52: 40.039 distance: 52 - 53: 34.185 distance: 53 - 54: 15.495 distance: 53 - 55: 33.684 distance: 55 - 56: 19.345 distance: 56 - 57: 32.493 distance: 56 - 59: 17.251 distance: 57 - 58: 43.890 distance: 57 - 60: 14.865 distance: 60 - 61: 17.510 distance: 61 - 62: 24.249 distance: 61 - 64: 53.698 distance: 62 - 63: 27.218 distance: 62 - 65: 43.256 distance: 65 - 66: 51.536 distance: 66 - 67: 56.580 distance: 66 - 69: 41.126 distance: 67 - 68: 39.810 distance: 70 - 71: 42.308 distance: 70 - 72: 46.808 distance: 71 - 73: 28.237 distance: 72 - 74: 14.420 distance: 73 - 74: 50.905 distance: 75 - 76: 40.122 distance: 76 - 77: 59.383 distance: 76 - 79: 55.014 distance: 77 - 78: 44.105 distance: 77 - 84: 40.270 distance: 79 - 80: 41.654 distance: 80 - 81: 26.923 distance: 81 - 82: 22.517 distance: 81 - 83: 46.109 distance: 84 - 85: 15.799 distance: 85 - 86: 21.830 distance: 85 - 88: 6.758 distance: 86 - 87: 45.354 distance: 86 - 95: 50.452 distance: 88 - 89: 24.786 distance: 89 - 90: 12.242 distance: 89 - 91: 26.702 distance: 90 - 92: 27.876 distance: 91 - 93: 31.862 distance: 92 - 94: 21.843 distance: 93 - 94: 22.700 distance: 95 - 96: 34.172 distance: 96 - 97: 45.744 distance: 96 - 99: 41.260 distance: 97 - 98: 25.071 distance: 97 - 102: 43.173 distance: 99 - 100: 41.294 distance: 99 - 101: 43.209 distance: 102 - 103: 44.586 distance: 103 - 104: 13.861 distance: 103 - 106: 44.642 distance: 104 - 105: 41.055 distance: 104 - 107: 22.830