Starting phenix.real_space_refine on Fri Aug 22 13:06:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ly0_23581/08_2025/7ly0_23581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ly0_23581/08_2025/7ly0_23581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ly0_23581/08_2025/7ly0_23581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ly0_23581/08_2025/7ly0_23581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ly0_23581/08_2025/7ly0_23581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ly0_23581/08_2025/7ly0_23581.map" } resolution = 2.6 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= 0.039 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 10 5.16 5 C 1796 2.51 5 N 463 2.21 5 O 536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 2805 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1033 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain breaks: 7 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 785 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.97, per 1000 atoms: 0.35 Number of scatterers: 2805 At special positions: 0 Unit cell: (73.5, 71.4, 74.55, 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 10 16.00 O 536 8.00 N 463 7.00 C 1796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 149 " " NAG B 1 " - " ASN A 17 " Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 109.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 650 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 7.6% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.185A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.544A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.445A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 95 Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.467A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.467A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.710A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.002A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) 103 hydrogen bonds defined for protein. 225 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: 0.38 Time building geometry restraints manager: 0.39 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: 520 1.32 - 1.45: 807 1.45 - 1.57: 1528 1.57 - 1.70: 4 1.70 - 1.82: 13 Bond restraints: 2872 Sorted by residual: bond pdb=" N TRP H 104 " pdb=" CA TRP H 104 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.16e-02 7.43e+03 8.17e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" CB ILE A 235 " pdb=" CG1 ILE A 235 " ideal model delta sigma weight residual 1.530 1.584 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" CG ASP A 138 " pdb=" OD1 ASP A 138 " ideal model delta sigma weight residual 1.249 1.198 0.051 1.90e-02 2.77e+03 7.23e+00 ... (remaining 2867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 3280 1.46 - 2.92: 518 2.92 - 4.38: 68 4.38 - 5.84: 25 5.84 - 7.30: 14 Bond angle restraints: 3905 Sorted by residual: angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 125.78 -6.12 7.30e-01 1.88e+00 7.02e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.32 -7.29 9.90e-01 1.02e+00 5.42e+01 angle pdb=" C ILE L 57 " pdb=" N PRO L 58 " pdb=" CA PRO L 58 " ideal model delta sigma weight residual 120.03 126.82 -6.79 9.90e-01 1.02e+00 4.71e+01 angle pdb=" C ARG L 53 " pdb=" N PRO L 54 " pdb=" CA PRO L 54 " ideal model delta sigma weight residual 119.92 127.22 -7.30 1.07e+00 8.73e-01 4.65e+01 angle pdb=" C PRO L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta sigma weight residual 119.19 126.17 -6.98 1.06e+00 8.90e-01 4.33e+01 ... (remaining 3900 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.83: 1668 17.83 - 35.65: 39 35.65 - 53.48: 14 53.48 - 71.30: 3 71.30 - 89.12: 1 Dihedral angle restraints: 1725 sinusoidal: 708 harmonic: 1017 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.87 41.13 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 87 " pdb=" CB CYS L 87 " ideal model delta sinusoidal sigma weight residual 93.00 55.35 37.65 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CA ARG L 53 " pdb=" C ARG L 53 " pdb=" N PRO L 54 " pdb=" CA PRO L 54 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 1722 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.062: 296 0.062 - 0.124: 104 0.124 - 0.186: 29 0.186 - 0.248: 16 0.248 - 0.309: 5 Chirality restraints: 450 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 -2.53 0.13 2.00e-02 2.50e+03 4.24e+01 chirality pdb=" C1 MAN B 3 " pdb=" O4 NAG B 2 " pdb=" C2 MAN B 3 " pdb=" O5 MAN B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.47 -0.07 2.00e-02 2.50e+03 1.19e+01 chirality pdb=" C1 FUC B 4 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 4 " pdb=" O5 FUC B 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.82e+00 ... (remaining 447 not shown) Planarity restraints: 484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 33 " 0.035 2.00e-02 2.50e+03 1.89e-02 7.18e+00 pdb=" CG TYR L 33 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR L 33 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR L 33 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR L 33 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR L 33 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR L 33 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 33 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 122 " 0.024 2.00e-02 2.50e+03 2.31e-02 6.67e+00 pdb=" CG ASN A 122 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 122 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 122 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 103 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C GLU H 103 " 0.032 2.00e-02 2.50e+03 pdb=" O GLU H 103 " -0.012 2.00e-02 2.50e+03 pdb=" N TRP H 104 " -0.011 2.00e-02 2.50e+03 ... (remaining 481 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1504 2.99 - 3.47: 2388 3.47 - 3.95: 4816 3.95 - 4.42: 5482 4.42 - 4.90: 8858 Nonbonded interactions: 23048 Sorted by model distance: nonbonded pdb=" NZ LYS A 77 " pdb=" O THR A 250 " model vdw 2.515 3.120 nonbonded pdb=" NZ LYS A 147 " pdb=" O LEU L 27 " model vdw 2.575 3.120 nonbonded pdb=" OD1 ASP L 91 " pdb=" N GLY L 94 " model vdw 2.576 3.120 nonbonded pdb=" OD1 ASP H 107 " pdb=" N TYR H 108 " model vdw 2.577 3.120 nonbonded pdb=" OG SER A 155 " pdb=" N GLU A 156 " model vdw 2.591 3.120 ... (remaining 23043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.730 Find NCS groups from input model: 0.010 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:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 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 : 0.012 0.067 2881 Z= 0.646 Angle : 1.198 7.298 3929 Z= 0.800 Chirality : 0.080 0.309 450 Planarity : 0.005 0.019 481 Dihedral : 9.438 89.124 1066 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.36 % Allowed : 0.36 % Favored : 99.29 % 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: 1.70 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 1.04 (0.39), residues: 154 loop : 1.42 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 246 TYR 0.035 0.004 TYR L 33 PHE 0.014 0.003 PHE A 175 TRP 0.014 0.004 TRP L 34 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.01191 ( 2872) covalent geometry : angle 1.18702 ( 3905) SS BOND : bond 0.00404 ( 3) SS BOND : angle 2.38100 ( 6) hydrogen bonds : bond 0.12230 ( 94) hydrogen bonds : angle 8.05201 ( 225) link_ALPHA1-4 : bond 0.06677 ( 1) link_ALPHA1-4 : angle 3.07699 ( 3) link_BETA1-4 : bond 0.06179 ( 1) link_BETA1-4 : angle 3.03880 ( 3) link_BETA1-6 : bond 0.04555 ( 1) link_BETA1-6 : angle 1.44181 ( 3) link_NAG-ASN : bond 0.05587 ( 3) link_NAG-ASN : angle 2.16031 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.105 Fit side-chains REVERT: A 19 THR cc_start: 0.7681 (m) cc_final: 0.7459 (m) REVERT: A 86 PHE cc_start: 0.8153 (t80) cc_final: 0.7943 (t80) REVERT: L 20 ILE cc_start: 0.7448 (mt) cc_final: 0.7151 (mp) REVERT: L 31 TYR cc_start: 0.8175 (m-80) cc_final: 0.7627 (m-80) REVERT: L 53 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7921 (mtm110) REVERT: L 86 TYR cc_start: 0.8811 (m-80) cc_final: 0.8570 (m-80) REVERT: L 98 VAL cc_start: 0.8630 (p) cc_final: 0.8395 (t) REVERT: H 18 LEU cc_start: 0.7209 (tt) cc_final: 0.7004 (tp) REVERT: H 27 PHE cc_start: 0.7322 (p90) cc_final: 0.6992 (p90) REVERT: H 45 LEU cc_start: 0.8886 (mt) cc_final: 0.8563 (mt) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.3167 time to fit residues: 31.8931 Evaluate side-chains 77 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 2 optimal weight: 0.0970 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 overall best weight: 0.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 245 HIS H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.189236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.183942 restraints weight = 2814.703| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 0.67 r_work: 0.3925 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2881 Z= 0.149 Angle : 0.579 6.263 3929 Z= 0.293 Chirality : 0.044 0.158 450 Planarity : 0.004 0.036 481 Dihedral : 4.629 21.007 504 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.50 % Allowed : 11.79 % Favored : 85.71 % 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: 1.69 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 1.19 (0.40), residues: 152 loop : 1.24 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 246 TYR 0.009 0.001 TYR H 60 PHE 0.008 0.001 PHE A 133 TRP 0.009 0.001 TRP L 34 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2872) covalent geometry : angle 0.56554 ( 3905) SS BOND : bond 0.00105 ( 3) SS BOND : angle 0.36749 ( 6) hydrogen bonds : bond 0.03402 ( 94) hydrogen bonds : angle 6.31819 ( 225) link_ALPHA1-4 : bond 0.01939 ( 1) link_ALPHA1-4 : angle 2.76808 ( 3) link_BETA1-4 : bond 0.00552 ( 1) link_BETA1-4 : angle 1.86853 ( 3) link_BETA1-6 : bond 0.00334 ( 1) link_BETA1-6 : angle 1.44138 ( 3) link_NAG-ASN : bond 0.00374 ( 3) link_NAG-ASN : angle 1.81018 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.113 Fit side-chains REVERT: A 19 THR cc_start: 0.8091 (m) cc_final: 0.7793 (m) REVERT: A 190 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6833 (mtt-85) REVERT: L 31 TYR cc_start: 0.8371 (m-80) cc_final: 0.7960 (m-80) outliers start: 7 outliers final: 4 residues processed: 90 average time/residue: 0.2996 time to fit residues: 27.9983 Evaluate side-chains 82 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.178649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.173184 restraints weight = 2815.311| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 0.66 r_work: 0.3802 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 2881 Z= 0.302 Angle : 0.726 7.107 3929 Z= 0.371 Chirality : 0.050 0.201 450 Planarity : 0.006 0.046 481 Dihedral : 5.271 21.057 504 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.64 % Allowed : 13.21 % Favored : 82.14 % 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: 0.41 (0.45), residues: 334 helix: None (None), residues: 0 sheet: 0.45 (0.42), residues: 137 loop : 0.26 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 246 TYR 0.017 0.002 TYR L 31 PHE 0.018 0.002 PHE A 133 TRP 0.006 0.001 TRP H 47 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00689 ( 2872) covalent geometry : angle 0.70389 ( 3905) SS BOND : bond 0.00383 ( 3) SS BOND : angle 2.58495 ( 6) hydrogen bonds : bond 0.04206 ( 94) hydrogen bonds : angle 6.53303 ( 225) link_ALPHA1-4 : bond 0.01931 ( 1) link_ALPHA1-4 : angle 2.54597 ( 3) link_BETA1-4 : bond 0.00547 ( 1) link_BETA1-4 : angle 1.75161 ( 3) link_BETA1-6 : bond 0.00178 ( 1) link_BETA1-6 : angle 1.16675 ( 3) link_NAG-ASN : bond 0.00166 ( 3) link_NAG-ASN : angle 2.60576 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.102 Fit side-chains REVERT: A 190 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6890 (mtt-85) REVERT: A 248 TYR cc_start: 0.8256 (t80) cc_final: 0.7983 (t80) REVERT: L 16 GLN cc_start: 0.6047 (mt0) cc_final: 0.5478 (mp10) REVERT: L 31 TYR cc_start: 0.8611 (m-80) cc_final: 0.7878 (m-80) REVERT: L 104 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8044 (ttpp) REVERT: H 27 PHE cc_start: 0.7589 (p90) cc_final: 0.7382 (p90) REVERT: H 45 LEU cc_start: 0.8733 (mt) cc_final: 0.8524 (mt) outliers start: 13 outliers final: 8 residues processed: 91 average time/residue: 0.3448 time to fit residues: 32.4185 Evaluate side-chains 84 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 0 optimal weight: 0.9990 chunk 6 optimal weight: 0.0970 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 33 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 overall best weight: 0.1978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.181650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.176173 restraints weight = 2780.293| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 0.67 r_work: 0.3830 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2881 Z= 0.151 Angle : 0.572 5.626 3929 Z= 0.295 Chirality : 0.044 0.162 450 Planarity : 0.004 0.040 481 Dihedral : 4.694 18.928 504 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 5.71 % Allowed : 15.00 % Favored : 79.29 % 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: 0.55 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.50 (0.42), residues: 143 loop : 0.39 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 16 TYR 0.012 0.001 TYR L 31 PHE 0.008 0.001 PHE A 133 TRP 0.005 0.001 TRP H 109 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 2872) covalent geometry : angle 0.55157 ( 3905) SS BOND : bond 0.00066 ( 3) SS BOND : angle 2.30884 ( 6) hydrogen bonds : bond 0.03277 ( 94) hydrogen bonds : angle 6.15082 ( 225) link_ALPHA1-4 : bond 0.01745 ( 1) link_ALPHA1-4 : angle 2.58772 ( 3) link_BETA1-4 : bond 0.00431 ( 1) link_BETA1-4 : angle 1.67633 ( 3) link_BETA1-6 : bond 0.00300 ( 1) link_BETA1-6 : angle 1.16002 ( 3) link_NAG-ASN : bond 0.00288 ( 3) link_NAG-ASN : angle 1.91184 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.083 Fit side-chains REVERT: A 190 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6810 (mtt-85) REVERT: A 248 TYR cc_start: 0.8248 (t80) cc_final: 0.7987 (t80) REVERT: L 31 TYR cc_start: 0.8466 (m-80) cc_final: 0.8256 (m-80) REVERT: L 104 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7728 (ttpp) outliers start: 16 outliers final: 10 residues processed: 80 average time/residue: 0.3543 time to fit residues: 29.2120 Evaluate side-chains 80 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 SER 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: 60.9416 > 50: distance: 26 - 30: 22.784 distance: 30 - 31: 26.877 distance: 31 - 32: 41.835 distance: 31 - 34: 22.940 distance: 32 - 33: 41.534 distance: 32 - 42: 36.205 distance: 34 - 35: 5.953 distance: 35 - 37: 5.892 distance: 36 - 38: 5.858 distance: 37 - 39: 7.344 distance: 40 - 41: 4.196 distance: 42 - 43: 18.768 distance: 43 - 44: 22.762 distance: 43 - 46: 9.036 distance: 44 - 45: 19.811 distance: 44 - 47: 17.557 distance: 47 - 48: 14.650 distance: 47 - 259: 13.217 distance: 48 - 49: 5.431 distance: 48 - 51: 7.329 distance: 49 - 50: 17.151 distance: 49 - 59: 12.638 distance: 50 - 256: 13.601 distance: 51 - 52: 8.617 distance: 52 - 54: 5.298 distance: 53 - 55: 3.265 distance: 54 - 56: 4.654 distance: 56 - 57: 4.398 distance: 59 - 60: 11.689 distance: 60 - 61: 6.610 distance: 60 - 63: 4.462 distance: 61 - 62: 12.972 distance: 61 - 73: 12.473 distance: 62 - 159: 8.945 distance: 63 - 64: 4.087 distance: 64 - 65: 4.530 distance: 64 - 66: 5.174 distance: 66 - 68: 12.826 distance: 66 - 69: 7.400 distance: 67 - 68: 12.713 distance: 68 - 70: 8.623 distance: 70 - 72: 3.969 distance: 71 - 72: 3.007 distance: 73 - 74: 25.256 distance: 73 - 243: 11.018 distance: 74 - 75: 40.088 distance: 74 - 77: 16.518 distance: 75 - 76: 22.398 distance: 75 - 85: 32.041 distance: 76 - 240: 8.722 distance: 77 - 78: 9.058 distance: 78 - 80: 4.168 distance: 85 - 86: 34.160 distance: 85 - 148: 16.968 distance: 86 - 87: 56.586 distance: 86 - 89: 31.337 distance: 87 - 88: 56.617 distance: 87 - 96: 29.358 distance: 88 - 145: 31.666 distance: 89 - 90: 16.558 distance: 90 - 91: 3.359 distance: 91 - 92: 7.217 distance: 92 - 93: 9.277 distance: 93 - 94: 7.364 distance: 93 - 95: 10.018 distance: 96 - 97: 33.273 distance: 96 - 224: 17.699 distance: 97 - 98: 51.809 distance: 97 - 100: 29.623 distance: 98 - 99: 42.574 distance: 98 - 105: 56.785 distance: 99 - 221: 12.108 distance: 100 - 101: 9.299 distance: 101 - 102: 7.433 distance: 102 - 103: 3.129 distance: 102 - 104: 3.097 distance: 105 - 106: 60.942 distance: 106 - 107: 59.477 distance: 106 - 109: 55.840 distance: 107 - 108: 53.215 distance: 107 - 114: 55.692 distance: 109 - 110: 31.164 distance: 110 - 111: 7.032 distance: 111 - 112: 13.322 distance: 112 - 113: 6.011 distance: 114 - 115: 44.927 distance: 114 - 120: 55.512 distance: 115 - 116: 45.920 distance: 115 - 118: 49.241 distance: 116 - 117: 46.368 distance: 116 - 121: 38.377 distance: 118 - 119: 20.608 distance: 119 - 120: 31.889 distance: 121 - 122: 28.905 distance: 122 - 123: 39.544 distance: 123 - 124: 34.130 distance: 123 - 125: 17.334