Starting phenix.real_space_refine on Sat Aug 23 06:25:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sn2_25209/08_2025/7sn2_25209_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sn2_25209/08_2025/7sn2_25209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sn2_25209/08_2025/7sn2_25209_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sn2_25209/08_2025/7sn2_25209_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sn2_25209/08_2025/7sn2_25209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sn2_25209/08_2025/7sn2_25209.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 3284 2.51 5 N 868 2.21 5 O 1016 1.98 5 H 4904 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10092 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3477 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 13, 'TRANS': 209} Chain: "H" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3236 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3251 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 89 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 1.98, per 1000 atoms: 0.20 Number of scatterers: 10092 At special positions: 0 Unit cell: (85.8, 113.85, 99, 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 20 16.00 O 1016 8.00 N 868 7.00 C 3284 6.00 H 4904 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 6 " BETA1-2 " MAN C 4 " - " NAG C 5 " " MAN C 6 " - " NAG C 7 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 1 " - " ASN A 331 " " NAG C 1 " - " ASN A 343 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 188.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 13 sheets defined 11.4% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 322 through 326 removed outlier: 4.062A pdb=" N SER A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 326 " --> pdb=" O THR A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 326' Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.084A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.690A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.562A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 187 through 192 removed outlier: 4.389A pdb=" N THR H 191 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.580A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 4.211A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.914A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.410A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.410A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 120 through 122 removed outlier: 5.924A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 120 through 122 removed outlier: 5.924A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.457A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL H 198 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL H 207 " --> pdb=" O VAL H 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.507A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.746A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 145 through 149 178 hydrogen bonds defined for protein. 426 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 4900 1.04 - 1.24: 685 1.24 - 1.44: 1708 1.44 - 1.64: 2905 1.64 - 1.85: 22 Bond restraints: 10220 Sorted by residual: bond pdb=" CA PHE A 329 " pdb=" CB PHE A 329 " ideal model delta sigma weight residual 1.530 1.569 -0.039 1.58e-02 4.01e+03 6.05e+00 bond pdb=" C2 MAN C 6 " pdb=" O2 MAN C 6 " ideal model delta sigma weight residual 1.407 1.454 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" CB THR A 385 " pdb=" CG2 THR A 385 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.88e+00 bond pdb=" CA ALA A 435 " pdb=" C ALA A 435 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.31e-02 5.83e+03 4.69e+00 bond pdb=" C6 BMA C 3 " pdb=" O6 BMA C 3 " ideal model delta sigma weight residual 1.411 1.453 -0.042 2.00e-02 2.50e+03 4.37e+00 ... (remaining 10215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 18125 4.17 - 8.33: 159 8.33 - 12.50: 20 12.50 - 16.67: 1 16.67 - 20.84: 3 Bond angle restraints: 18308 Sorted by residual: angle pdb=" N LYS A 529 " pdb=" CA LYS A 529 " pdb=" C LYS A 529 " ideal model delta sigma weight residual 111.02 120.97 -9.95 1.22e+00 6.72e-01 6.65e+01 angle pdb=" N ASN A 437 " pdb=" CA ASN A 437 " pdb=" CB ASN A 437 " ideal model delta sigma weight residual 109.97 98.40 11.57 1.47e+00 4.63e-01 6.20e+01 angle pdb=" HB2 ASN A 437 " pdb=" CB ASN A 437 " pdb=" HB3 ASN A 437 " ideal model delta sigma weight residual 110.00 89.16 20.84 3.00e+00 1.11e-01 4.82e+01 angle pdb=" CG ASN A 437 " pdb=" CB ASN A 437 " pdb=" HB2 ASN A 437 " ideal model delta sigma weight residual 108.00 87.44 20.56 3.00e+00 1.11e-01 4.70e+01 angle pdb=" CA ASN A 437 " pdb=" CB ASN A 437 " pdb=" HB2 ASN A 437 " ideal model delta sigma weight residual 109.00 88.49 20.51 3.00e+00 1.11e-01 4.67e+01 ... (remaining 18303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.01: 4717 25.01 - 50.02: 278 50.02 - 75.03: 48 75.03 - 100.04: 17 100.04 - 125.05: 9 Dihedral angle restraints: 5069 sinusoidal: 2787 harmonic: 2282 Sorted by residual: dihedral pdb=" CA SER A 530 " pdb=" C SER A 530 " pdb=" N THR A 531 " pdb=" CA THR A 531 " ideal model delta harmonic sigma weight residual 180.00 136.70 43.30 0 5.00e+00 4.00e-02 7.50e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 17.59 75.41 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CA VAL A 395 " pdb=" C VAL A 395 " pdb=" N TYR A 396 " pdb=" CA TYR A 396 " ideal model delta harmonic sigma weight residual -180.00 -143.39 -36.61 0 5.00e+00 4.00e-02 5.36e+01 ... (remaining 5066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 756 0.118 - 0.237: 61 0.237 - 0.355: 8 0.355 - 0.474: 1 0.474 - 0.592: 1 Chirality restraints: 827 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.34e+02 chirality pdb=" C1 NAG C 7 " pdb=" O2 MAN C 6 " pdb=" C2 NAG C 7 " pdb=" O5 NAG C 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.05e+02 chirality pdb=" C1 NAG C 5 " pdb=" O2 MAN C 4 " pdb=" C2 NAG C 5 " pdb=" O5 NAG C 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 2.01e+02 ... (remaining 824 not shown) Planarity restraints: 1529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 91 " 0.527 9.50e-02 1.11e+02 1.76e-01 3.40e+01 pdb=" NE ARG L 91 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG L 91 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG L 91 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG L 91 " 0.017 2.00e-02 2.50e+03 pdb="HH11 ARG L 91 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG L 91 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG L 91 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG L 91 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 99 " 0.022 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C ARG H 99 " -0.075 2.00e-02 2.50e+03 pdb=" O ARG H 99 " 0.029 2.00e-02 2.50e+03 pdb=" N ASP H 100 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 94 " -0.371 9.50e-02 1.11e+02 1.24e-01 1.67e+01 pdb=" NE ARG H 94 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG H 94 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG H 94 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 94 " -0.010 2.00e-02 2.50e+03 pdb="HH11 ARG H 94 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG H 94 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG H 94 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 94 " -0.001 2.00e-02 2.50e+03 ... (remaining 1526 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 195 2.11 - 2.73: 16965 2.73 - 3.35: 27854 3.35 - 3.98: 35537 3.98 - 4.60: 53717 Nonbonded interactions: 134268 Sorted by model distance: nonbonded pdb=" O ALA A 372 " pdb="HH22 ARG H 100D" model vdw 1.482 2.450 nonbonded pdb="HD21 ASN A 370 " pdb=" HH TYR H 58 " model vdw 1.545 2.100 nonbonded pdb="HH22 ARG A 328 " pdb=" O LYS A 528 " model vdw 1.611 2.450 nonbonded pdb=" H SER H 156 " pdb=" OD1 ASN H 197 " model vdw 1.680 2.450 nonbonded pdb=" H LYS A 462 " pdb=" OE2 GLU A 465 " model vdw 1.686 2.450 ... (remaining 134263 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: 1.280 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: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.980 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 5334 Z= 0.329 Angle : 1.350 15.901 7282 Z= 0.720 Chirality : 0.073 0.592 827 Planarity : 0.013 0.236 916 Dihedral : 17.661 125.050 2052 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 0.78 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -1.92 (0.32), residues: 642 helix: -2.74 (0.79), residues: 32 sheet: -0.58 (0.35), residues: 222 loop : -1.61 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 105 TYR 0.052 0.004 TYR A 508 PHE 0.047 0.004 PHE A 329 TRP 0.032 0.003 TRP A 436 HIS 0.009 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00716 ( 5316) covalent geometry : angle 1.30779 ( 7236) SS BOND : bond 0.01193 ( 8) SS BOND : angle 2.19704 ( 16) hydrogen bonds : bond 0.17229 ( 156) hydrogen bonds : angle 10.40459 ( 426) link_ALPHA1-3 : bond 0.00432 ( 1) link_ALPHA1-3 : angle 3.77049 ( 3) link_ALPHA1-6 : bond 0.01257 ( 1) link_ALPHA1-6 : angle 5.46797 ( 3) link_BETA1-2 : bond 0.00930 ( 2) link_BETA1-2 : angle 5.10887 ( 6) link_BETA1-4 : bond 0.01310 ( 4) link_BETA1-4 : angle 5.86693 ( 12) link_NAG-ASN : bond 0.00753 ( 2) link_NAG-ASN : angle 4.37503 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7930 (m-30) cc_final: 0.7577 (m-30) REVERT: A 428 ASP cc_start: 0.8175 (t70) cc_final: 0.7962 (t70) REVERT: H 34 MET cc_start: 0.7390 (mmt) cc_final: 0.7135 (mmt) REVERT: H 46 GLU cc_start: 0.7527 (tt0) cc_final: 0.6897 (pt0) REVERT: L 13 LEU cc_start: 0.7664 (tp) cc_final: 0.7427 (tp) REVERT: L 189 HIS cc_start: 0.6327 (t-90) cc_final: 0.5909 (t70) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1453 time to fit residues: 26.2274 Evaluate side-chains 117 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.2047 > 50: distance: 51 - 67: 12.244 distance: 67 - 68: 17.231 distance: 67 - 74: 13.096 distance: 68 - 69: 7.759 distance: 68 - 71: 26.861 distance: 68 - 75: 16.121 distance: 69 - 70: 26.957 distance: 69 - 81: 14.431 distance: 71 - 72: 25.349 distance: 71 - 73: 8.743 distance: 71 - 76: 18.692 distance: 72 - 77: 34.985 distance: 73 - 78: 23.877 distance: 73 - 79: 16.197 distance: 73 - 80: 16.927 distance: 81 - 82: 7.716 distance: 81 - 87: 14.869 distance: 82 - 83: 30.411 distance: 82 - 85: 21.716 distance: 82 - 88: 23.016 distance: 83 - 84: 20.738 distance: 83 - 92: 10.880 distance: 85 - 86: 10.939 distance: 85 - 89: 24.734 distance: 86 - 91: 7.657 distance: 92 - 93: 20.897 distance: 92 - 96: 20.924 distance: 93 - 94: 51.409 distance: 93 - 97: 9.979 distance: 93 - 98: 30.993 distance: 94 - 95: 53.962 distance: 94 - 99: 57.158 distance: 99 - 100: 58.598 distance: 99 - 106: 32.227 distance: 100 - 101: 54.235 distance: 100 - 103: 46.226 distance: 100 - 107: 45.513 distance: 101 - 102: 19.034 distance: 101 - 115: 36.914 distance: 103 - 104: 19.200 distance: 103 - 105: 24.132 distance: 103 - 108: 21.265 distance: 104 - 109: 24.136 distance: 104 - 110: 29.859 distance: 104 - 111: 28.448 distance: 105 - 112: 31.013 distance: 105 - 113: 22.163 distance: 105 - 114: 10.155 distance: 115 - 116: 23.296 distance: 115 - 125: 18.265 distance: 115 - 283: 22.991 distance: 116 - 117: 14.658 distance: 116 - 119: 16.391 distance: 116 - 126: 21.128 distance: 117 - 118: 34.382 distance: 117 - 132: 31.428 distance: 118 - 280: 27.197 distance: 119 - 120: 26.174 distance: 119 - 127: 15.811 distance: 119 - 128: 7.701 distance: 120 - 121: 55.769 distance: 120 - 122: 63.893 distance: 121 - 123: 34.759 distance: 122 - 124: 54.637 distance: 122 - 129: 40.687 distance: 123 - 124: 45.734 distance: 123 - 130: 27.921 distance: 124 - 131: 28.739 distance: 132 - 133: 41.609 distance: 132 - 139: 41.778 distance: 133 - 134: 30.836 distance: 133 - 136: 33.830 distance: 133 - 140: 47.752 distance: 134 - 135: 26.600 distance: 134 - 146: 23.632 distance: 136 - 137: 33.833 distance: 136 - 138: 18.338 distance: 136 - 141: 28.747 distance: 137 - 142: 39.998 distance: 138 - 143: 17.840 distance: 138 - 144: 18.353 distance: 138 - 145: 27.090 distance: 146 - 147: 39.099 distance: 146 - 157: 29.749 distance: 147 - 148: 47.810 distance: 147 - 150: 46.933 distance: 147 - 158: 48.112 distance: 148 - 149: 39.267 distance: 148 - 166: 50.190 distance: 150 - 151: 28.307 distance: 150 - 159: 41.910 distance: 150 - 160: 31.951 distance: 151 - 152: 10.951 distance: 151 - 153: 17.964 distance: 152 - 154: 10.601 distance: 152 - 161: 17.488 distance: 153 - 155: 9.601 distance: 153 - 162: 20.661 distance: 154 - 156: 14.317 distance: 154 - 163: 18.085 distance: 155 - 156: 18.422 distance: 155 - 164: 28.263 distance: 156 - 165: 26.857 distance: 166 - 167: 32.862 distance: 166 - 172: 32.310 distance: 167 - 168: 55.363 distance: 167 - 170: 24.359 distance: 167 - 173: 25.171 distance: 168 - 169: 40.987 distance: 168 - 180: 50.318 distance: 170 - 171: 15.579 distance: 170 - 174: 20.116 distance: 170 - 175: 35.229 distance: 171 - 172: 12.033 distance: 171 - 176: 29.058 distance: 171 - 177: 25.455 distance: 172 - 178: 18.084 distance: 172 - 179: 14.604 distance: 180 - 181: 34.251 distance: 180 - 185: 38.087 distance: 181 - 182: 38.180 distance: 181 - 184: 11.773 distance: 181 - 186: 21.226 distance: 182 - 183: 32.638 distance: 182 - 190: 42.601 distance: 184 - 187: 17.676 distance: 184 - 188: 23.235 distance: 184 - 189: 21.095 distance: 190 - 191: 22.315 distance: 190 - 197: 24.647 distance: 190 - 241: 18.838 distance: 191 - 192: 10.394 distance: 191 - 194: 5.158 distance: 191 - 198: 17.311 distance: 192 - 193: 14.376 distance: 192 - 206: 10.706 distance: 193 - 238: 14.388 distance: 194 - 195: 13.856 distance: 194 - 196: 5.485 distance: 194 - 199: 19.178 distance: 195 - 200: 11.082 distance: 195 - 201: 9.002 distance: 195 - 202: 14.264 distance: 196 - 203: 10.637 distance: 196 - 204: 10.850 distance: 196 - 205: 5.851