Starting phenix.real_space_refine on Tue Feb 3 14:16:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ucp_64050/02_2026/9ucp_64050_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ucp_64050/02_2026/9ucp_64050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ucp_64050/02_2026/9ucp_64050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ucp_64050/02_2026/9ucp_64050.map" model { file = "/net/cci-nas-00/data/ceres_data/9ucp_64050/02_2026/9ucp_64050_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ucp_64050/02_2026/9ucp_64050_neut.cif" } resolution = 2.88 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= 0.001 sd= 0.079 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 20 5.16 5 C 2265 2.51 5 N 598 2.21 5 O 646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3529 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2601 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 13, 'TRANS': 359} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 474 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 8, 'PHE:plan': 4, 'TRP:plan': 1, 'GLN:plan1': 4, 'TYR:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 216 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 698 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 4, 'ARG:plan': 4, 'PHE:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 149 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'IXO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.01, per 1000 atoms: 0.29 Number of scatterers: 3529 At special positions: 0 Unit cell: (53.0425, 63.8675, 122.322, 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 20 16.00 O 646 8.00 N 598 7.00 C 2265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS A 351 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 158.2 milliseconds 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 3 sheets defined 69.1% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 24 through 53 removed outlier: 4.230A pdb=" N PHE A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 61 through 88 removed outlier: 4.501A pdb=" N MET A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASN A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 129 removed outlier: 4.079A pdb=" N ALA A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.704A pdb=" N ARG A 134 " --> pdb=" O PRO A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 168 removed outlier: 3.527A pdb=" N SER A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 5.358A pdb=" N GLN A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 197 through 232 removed outlier: 3.534A pdb=" N GLU A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 247 removed outlier: 4.143A pdb=" N THR A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 262 removed outlier: 3.525A pdb=" N ALA A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 removed outlier: 3.703A pdb=" N ALA A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.550A pdb=" N ALA A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 309 removed outlier: 3.595A pdb=" N LYS A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 302 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 351 removed outlier: 3.704A pdb=" N PHE A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Proline residue: A 340 - end of helix removed outlier: 3.551A pdb=" N PHE A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.716A pdb=" N CYS A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.608A pdb=" N THR A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.642A pdb=" N LEU A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 356 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 102 through 106 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.524A pdb=" N GLN C 5 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 59 removed outlier: 3.647A pdb=" N ASN C 58 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG C 38 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET C 34 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR C 37 " --> pdb=" O TYR C 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 69 through 72 252 hydrogen bonds defined for protein. 735 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: 0.52 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 572 1.31 - 1.44: 989 1.44 - 1.56: 2006 1.56 - 1.69: 0 1.69 - 1.82: 29 Bond restraints: 3596 Sorted by residual: bond pdb=" C10 IXO A 500 " pdb=" N11 IXO A 500 " ideal model delta sigma weight residual 1.270 1.450 -0.180 2.00e-02 2.50e+03 8.14e+01 bond pdb=" C05 IXO A 500 " pdb=" C06 IXO A 500 " ideal model delta sigma weight residual 1.450 1.528 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C10 IXO A 500 " pdb=" O09 IXO A 500 " ideal model delta sigma weight residual 1.325 1.399 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C07 IXO A 500 " pdb=" C08 IXO A 500 " ideal model delta sigma weight residual 1.454 1.527 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C05 IXO A 500 " pdb=" N02 IXO A 500 " ideal model delta sigma weight residual 1.504 1.451 0.053 2.00e-02 2.50e+03 6.95e+00 ... (remaining 3591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 4775 1.63 - 3.26: 123 3.26 - 4.89: 24 4.89 - 6.52: 8 6.52 - 8.15: 4 Bond angle restraints: 4934 Sorted by residual: angle pdb=" N TYR C 33 " pdb=" CA TYR C 33 " pdb=" C TYR C 33 " ideal model delta sigma weight residual 107.61 115.45 -7.84 1.74e+00 3.30e-01 2.03e+01 angle pdb=" N HIS A 90 " pdb=" CA HIS A 90 " pdb=" CB HIS A 90 " ideal model delta sigma weight residual 111.39 103.79 7.60 1.75e+00 3.27e-01 1.89e+01 angle pdb=" C GLN C 105 " pdb=" CA GLN C 105 " pdb=" CB GLN C 105 " ideal model delta sigma weight residual 111.95 106.27 5.68 1.50e+00 4.44e-01 1.43e+01 angle pdb=" N ARG C 106 " pdb=" CA ARG C 106 " pdb=" C ARG C 106 " ideal model delta sigma weight residual 113.16 117.83 -4.67 1.24e+00 6.50e-01 1.42e+01 angle pdb=" CA GLN C 105 " pdb=" C GLN C 105 " pdb=" O GLN C 105 " ideal model delta sigma weight residual 122.03 118.13 3.90 1.17e+00 7.31e-01 1.11e+01 ... (remaining 4929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.66: 1881 13.66 - 27.32: 138 27.32 - 40.97: 62 40.97 - 54.63: 10 54.63 - 68.29: 4 Dihedral angle restraints: 2095 sinusoidal: 593 harmonic: 1502 Sorted by residual: dihedral pdb=" CB CYS A 351 " pdb=" SG CYS A 351 " pdb=" SG CYS A 354 " pdb=" CB CYS A 354 " ideal model delta sinusoidal sigma weight residual -86.00 -124.42 38.42 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" N HIS A 90 " pdb=" C HIS A 90 " pdb=" CA HIS A 90 " pdb=" CB HIS A 90 " ideal model delta harmonic sigma weight residual 122.80 113.06 9.74 0 2.50e+00 1.60e-01 1.52e+01 dihedral pdb=" CA THR C 50 " pdb=" C THR C 50 " pdb=" N ILE C 51 " pdb=" CA ILE C 51 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 2092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 507 0.056 - 0.111: 82 0.111 - 0.167: 7 0.167 - 0.222: 1 0.222 - 0.278: 3 Chirality restraints: 600 Sorted by residual: chirality pdb=" CA HIS A 90 " pdb=" N HIS A 90 " pdb=" C HIS A 90 " pdb=" CB HIS A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA VAL C 104 " pdb=" N VAL C 104 " pdb=" C VAL C 104 " pdb=" CB VAL C 104 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA GLN C 105 " pdb=" N GLN C 105 " pdb=" C GLN C 105 " pdb=" CB GLN C 105 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 597 not shown) Planarity restraints: 625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 89 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.88e+00 pdb=" C GLY A 89 " -0.052 2.00e-02 2.50e+03 pdb=" O GLY A 89 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS A 90 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 158 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 159 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 199 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 200 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " -0.019 5.00e-02 4.00e+02 ... (remaining 622 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 1642 2.97 - 3.45: 3760 3.45 - 3.93: 5652 3.93 - 4.42: 6665 4.42 - 4.90: 10610 Nonbonded interactions: 28329 Sorted by model distance: nonbonded pdb=" O MET A 344 " pdb=" OG SER A 348 " model vdw 2.484 3.040 nonbonded pdb=" O VAL C 104 " pdb=" C GLN C 105 " model vdw 2.487 3.270 nonbonded pdb=" O LYS A 352 " pdb=" O ARG C 106 " model vdw 2.533 3.040 nonbonded pdb=" O ASN B 357 " pdb=" OD1 ASN B 357 " model vdw 2.541 3.040 nonbonded pdb=" CB SER A 348 " pdb=" NH1 ARG C 106 " model vdw 2.565 3.520 ... (remaining 28324 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: 1.150 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.680 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.180 3599 Z= 0.254 Angle : 0.695 8.145 4940 Z= 0.404 Chirality : 0.046 0.278 600 Planarity : 0.004 0.035 625 Dihedral : 12.703 68.288 1114 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.42 % Allowed : 1.07 % Favored : 97.51 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.35), residues: 501 helix: -0.43 (0.27), residues: 321 sheet: -3.39 (0.80), residues: 39 loop : -2.43 (0.46), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 99 TYR 0.017 0.001 TYR C 37 PHE 0.013 0.001 PHE A 197 TRP 0.009 0.001 TRP A 338 HIS 0.008 0.003 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 3596) covalent geometry : angle 0.69555 ( 4934) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.58827 ( 6) hydrogen bonds : bond 0.20161 ( 252) hydrogen bonds : angle 8.69403 ( 735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.076 Fit side-chains REVERT: A 285 GLU cc_start: 0.7183 (pt0) cc_final: 0.6923 (pt0) REVERT: A 322 LYS cc_start: 0.7313 (tttt) cc_final: 0.6898 (ttmm) REVERT: C 79 TYR cc_start: 0.6543 (m-80) cc_final: 0.5629 (t80) outliers start: 4 outliers final: 0 residues processed: 72 average time/residue: 0.5503 time to fit residues: 40.7635 Evaluate side-chains 54 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.0170 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN C 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.216085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.194975 restraints weight = 4232.281| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 1.54 r_work: 0.4095 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.4006 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3599 Z= 0.145 Angle : 0.586 6.202 4940 Z= 0.317 Chirality : 0.043 0.158 600 Planarity : 0.005 0.042 625 Dihedral : 4.712 23.129 555 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.78 % Allowed : 11.03 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.37), residues: 501 helix: 0.85 (0.28), residues: 327 sheet: -2.87 (0.93), residues: 28 loop : -2.65 (0.44), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 171 TYR 0.025 0.001 TYR C 33 PHE 0.018 0.001 PHE A 197 TRP 0.010 0.001 TRP A 360 HIS 0.006 0.003 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3596) covalent geometry : angle 0.58637 ( 4934) SS BOND : bond 0.00368 ( 3) SS BOND : angle 0.66275 ( 6) hydrogen bonds : bond 0.03965 ( 252) hydrogen bonds : angle 4.94227 ( 735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.136 Fit side-chains REVERT: A 170 GLU cc_start: 0.6716 (tt0) cc_final: 0.5710 (mt-10) REVERT: A 228 LYS cc_start: 0.7649 (ttmm) cc_final: 0.7399 (ttmm) REVERT: A 262 ASN cc_start: 0.6642 (m-40) cc_final: 0.6054 (t0) REVERT: A 285 GLU cc_start: 0.6852 (pt0) cc_final: 0.6479 (tp30) REVERT: B 350 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8432 (mm-40) REVERT: C 79 TYR cc_start: 0.6570 (m-80) cc_final: 0.5790 (t80) REVERT: C 101 TYR cc_start: 0.6942 (p90) cc_final: 0.6584 (p90) outliers start: 5 outliers final: 2 residues processed: 57 average time/residue: 0.4637 time to fit residues: 27.4464 Evaluate side-chains 47 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 373 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.215037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.194032 restraints weight = 4208.613| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 1.53 r_work: 0.4125 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3599 Z= 0.165 Angle : 0.594 7.114 4940 Z= 0.315 Chirality : 0.044 0.311 600 Planarity : 0.004 0.031 625 Dihedral : 4.734 22.546 555 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.20 % Allowed : 12.46 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.37), residues: 501 helix: 1.02 (0.28), residues: 331 sheet: -2.38 (1.12), residues: 21 loop : -2.92 (0.42), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 171 TYR 0.017 0.001 TYR C 101 PHE 0.016 0.002 PHE A 197 TRP 0.009 0.001 TRP A 360 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3596) covalent geometry : angle 0.59454 ( 4934) SS BOND : bond 0.00247 ( 3) SS BOND : angle 0.44478 ( 6) hydrogen bonds : bond 0.04040 ( 252) hydrogen bonds : angle 4.79721 ( 735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.133 Fit side-chains REVERT: A 170 GLU cc_start: 0.6673 (tt0) cc_final: 0.5682 (mt-10) REVERT: A 183 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5661 (tt) REVERT: A 262 ASN cc_start: 0.6666 (m-40) cc_final: 0.6123 (t0) REVERT: A 285 GLU cc_start: 0.6886 (pt0) cc_final: 0.6539 (tp30) REVERT: B 350 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8491 (mm-40) REVERT: C 34 MET cc_start: 0.7496 (ttm) cc_final: 0.7200 (mtp) REVERT: C 79 TYR cc_start: 0.6715 (m-80) cc_final: 0.5889 (t80) outliers start: 9 outliers final: 4 residues processed: 50 average time/residue: 0.4284 time to fit residues: 22.3006 Evaluate side-chains 49 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 33 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 0.0870 chunk 39 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN C 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.215036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.194099 restraints weight = 4192.419| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.53 r_work: 0.4089 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3998 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3599 Z= 0.167 Angle : 0.595 7.114 4940 Z= 0.315 Chirality : 0.044 0.311 600 Planarity : 0.004 0.031 625 Dihedral : 4.738 22.546 555 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.14 % Allowed : 13.52 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.37), residues: 501 helix: 1.02 (0.28), residues: 331 sheet: -2.38 (1.12), residues: 21 loop : -2.92 (0.42), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 171 TYR 0.017 0.001 TYR C 101 PHE 0.016 0.002 PHE A 197 TRP 0.009 0.001 TRP A 360 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3596) covalent geometry : angle 0.59533 ( 4934) SS BOND : bond 0.00247 ( 3) SS BOND : angle 0.44477 ( 6) hydrogen bonds : bond 0.04040 ( 252) hydrogen bonds : angle 4.79721 ( 735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.169 Fit side-chains REVERT: A 170 GLU cc_start: 0.6685 (tt0) cc_final: 0.5696 (mt-10) REVERT: A 183 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.5679 (tt) REVERT: A 262 ASN cc_start: 0.6693 (m-40) cc_final: 0.6124 (t0) REVERT: A 285 GLU cc_start: 0.6902 (pt0) cc_final: 0.6537 (tp30) REVERT: B 350 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8488 (mm-40) REVERT: C 34 MET cc_start: 0.7488 (ttm) cc_final: 0.7192 (mtp) REVERT: C 79 TYR cc_start: 0.6733 (m-80) cc_final: 0.5883 (t80) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.5242 time to fit residues: 25.0069 Evaluate side-chains 49 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 33 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 4 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: A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.215036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.194122 restraints weight = 4178.221| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 1.53 r_work: 0.4089 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3997 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3599 Z= 0.167 Angle : 0.595 7.114 4940 Z= 0.315 Chirality : 0.044 0.311 600 Planarity : 0.004 0.031 625 Dihedral : 4.734 22.546 555 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.14 % Allowed : 13.52 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.37), residues: 501 helix: 1.02 (0.28), residues: 331 sheet: -2.38 (1.12), residues: 21 loop : -2.92 (0.42), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 171 TYR 0.017 0.001 TYR C 101 PHE 0.016 0.002 PHE A 197 TRP 0.009 0.001 TRP A 360 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3596) covalent geometry : angle 0.59533 ( 4934) SS BOND : bond 0.00247 ( 3) SS BOND : angle 0.44477 ( 6) hydrogen bonds : bond 0.04040 ( 252) hydrogen bonds : angle 4.79721 ( 735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.136 Fit side-chains REVERT: A 170 GLU cc_start: 0.6684 (tt0) cc_final: 0.5694 (mt-10) REVERT: A 183 LEU cc_start: 0.5933 (OUTLIER) cc_final: 0.5681 (tt) REVERT: A 262 ASN cc_start: 0.6690 (m-40) cc_final: 0.6116 (t0) REVERT: A 285 GLU cc_start: 0.6912 (pt0) cc_final: 0.6534 (tp30) REVERT: B 350 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8489 (mm-40) REVERT: C 34 MET cc_start: 0.7490 (ttm) cc_final: 0.7192 (mtp) REVERT: C 79 TYR cc_start: 0.6734 (m-80) cc_final: 0.5876 (t80) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.5072 time to fit residues: 24.1846 Evaluate side-chains 49 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 33 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.4372 > 50: distance: 2 - 22: 20.742 distance: 6 - 33: 23.459 distance: 10 - 45: 26.725 distance: 17 - 22: 23.583 distance: 18 - 56: 31.399 distance: 22 - 23: 4.871 distance: 23 - 24: 11.522 distance: 23 - 26: 42.030 distance: 24 - 25: 30.623 distance: 24 - 33: 12.907 distance: 25 - 62: 18.157 distance: 26 - 27: 31.974 distance: 27 - 28: 31.080 distance: 28 - 29: 28.446 distance: 29 - 30: 4.907 distance: 30 - 31: 11.251 distance: 30 - 32: 9.985 distance: 33 - 34: 21.291 distance: 34 - 35: 13.247 distance: 34 - 37: 22.260 distance: 35 - 36: 15.586 distance: 35 - 45: 8.134 distance: 36 - 69: 16.552 distance: 37 - 38: 23.716 distance: 38 - 39: 6.555 distance: 38 - 40: 18.569 distance: 39 - 41: 23.026 distance: 40 - 42: 9.669 distance: 41 - 43: 24.753 distance: 42 - 43: 22.970 distance: 43 - 44: 19.796 distance: 45 - 46: 19.240 distance: 46 - 47: 13.491 distance: 46 - 49: 29.212 distance: 47 - 48: 19.457 distance: 47 - 56: 39.534 distance: 48 - 76: 49.382 distance: 49 - 50: 21.532 distance: 50 - 51: 8.848 distance: 50 - 52: 11.874 distance: 51 - 53: 16.004 distance: 52 - 54: 30.505 distance: 53 - 55: 22.437 distance: 54 - 55: 25.713 distance: 56 - 57: 19.224 distance: 57 - 58: 23.483 distance: 57 - 60: 15.524 distance: 58 - 59: 27.326 distance: 58 - 62: 23.184 distance: 60 - 61: 20.117 distance: 62 - 63: 47.405 distance: 63 - 64: 33.439 distance: 63 - 66: 24.156 distance: 64 - 65: 25.309 distance: 64 - 69: 35.597 distance: 66 - 67: 22.994 distance: 66 - 68: 33.347 distance: 69 - 70: 23.886 distance: 70 - 71: 22.527 distance: 70 - 73: 15.381 distance: 71 - 72: 13.074 distance: 71 - 76: 9.625 distance: 73 - 74: 45.037 distance: 73 - 75: 37.239 distance: 76 - 77: 35.532 distance: 77 - 78: 6.641 distance: 77 - 80: 12.760 distance: 78 - 79: 25.798 distance: 78 - 81: 19.080 distance: 79 - 102: 5.202 distance: 81 - 82: 15.764 distance: 81 - 87: 19.570 distance: 82 - 83: 25.697 distance: 82 - 85: 11.616 distance: 83 - 84: 14.131 distance: 83 - 88: 19.006 distance: 85 - 86: 33.259 distance: 86 - 87: 18.715 distance: 88 - 89: 4.304 distance: 89 - 90: 11.590 distance: 89 - 92: 9.512 distance: 90 - 91: 15.320 distance: 90 - 96: 10.899 distance: 91 - 124: 7.553 distance: 92 - 93: 13.647 distance: 93 - 94: 24.879 distance: 93 - 95: 20.373 distance: 96 - 97: 5.231 distance: 97 - 98: 16.251 distance: 97 - 100: 18.216 distance: 98 - 99: 8.217 distance: 98 - 102: 8.519 distance: 99 - 128: 7.580 distance: 100 - 101: 10.117