Starting phenix.real_space_refine on Mon Jan 13 14:38:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3o_44147/01_2025/9b3o_44147.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3o_44147/01_2025/9b3o_44147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3o_44147/01_2025/9b3o_44147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3o_44147/01_2025/9b3o_44147.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3o_44147/01_2025/9b3o_44147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3o_44147/01_2025/9b3o_44147.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.038 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 15 5.16 5 C 1770 2.51 5 N 406 2.21 5 O 439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 2630 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2630 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 12, 'TRANS': 350} Chain breaks: 3 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 2.63, per 1000 atoms: 1.00 Number of scatterers: 2630 At special positions: 0 Unit cell: (60.225, 69.3, 80.85, 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 15 16.00 O 439 8.00 N 406 7.00 C 1770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.95 Conformation dependent library (CDL) restraints added in 347.0 milliseconds 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 652 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 92.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 2 through 21 removed outlier: 4.052A pdb=" N PHE A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY A 20 " --> pdb=" O PHE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 removed outlier: 4.217A pdb=" N VAL A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 65 removed outlier: 3.897A pdb=" N LEU A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Proline residue: A 56 - end of helix Processing helix chain 'A' and resid 68 through 88 removed outlier: 3.984A pdb=" N CYS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 119 Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 127 through 152 Proline residue: A 144 - end of helix removed outlier: 3.716A pdb=" N GLU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 175 Processing helix chain 'A' and resid 204 through 233 removed outlier: 3.705A pdb=" N ILE A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 266 removed outlier: 6.384A pdb=" N ASP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LYS A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 288 Processing helix chain 'A' and resid 291 through 302 removed outlier: 3.678A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 321 Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 324 through 354 Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 356 through 390 244 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 784 1.34 - 1.46: 651 1.46 - 1.58: 1230 1.58 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 2694 Sorted by residual: bond pdb=" CG PRO A 24 " pdb=" CD PRO A 24 " ideal model delta sigma weight residual 1.503 1.478 0.025 3.40e-02 8.65e+02 5.34e-01 bond pdb=" CG PRO A 311 " pdb=" CD PRO A 311 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.96e-01 bond pdb=" CB PRO A 207 " pdb=" CG PRO A 207 " ideal model delta sigma weight residual 1.492 1.462 0.030 5.00e-02 4.00e+02 3.66e-01 bond pdb=" C PHE A 306 " pdb=" O PHE A 306 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.19e-02 7.06e+03 3.63e-01 bond pdb=" CG PRO A 121 " pdb=" CD PRO A 121 " ideal model delta sigma weight residual 1.503 1.483 0.020 3.40e-02 8.65e+02 3.47e-01 ... (remaining 2689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 3607 1.78 - 3.56: 39 3.56 - 5.34: 13 5.34 - 7.13: 3 7.13 - 8.91: 3 Bond angle restraints: 3665 Sorted by residual: angle pdb=" C GLY A 66 " pdb=" N LYS A 67 " pdb=" CA LYS A 67 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.17e+00 angle pdb=" CA LEU A 65 " pdb=" CB LEU A 65 " pdb=" CG LEU A 65 " ideal model delta sigma weight residual 116.30 125.21 -8.91 3.50e+00 8.16e-02 6.48e+00 angle pdb=" CA LEU A 386 " pdb=" CB LEU A 386 " pdb=" CG LEU A 386 " ideal model delta sigma weight residual 116.30 124.56 -8.26 3.50e+00 8.16e-02 5.58e+00 angle pdb=" CB MET A 95 " pdb=" CG MET A 95 " pdb=" SD MET A 95 " ideal model delta sigma weight residual 112.70 119.32 -6.62 3.00e+00 1.11e-01 4.88e+00 angle pdb=" CA LEU A 69 " pdb=" CB LEU A 69 " pdb=" CG LEU A 69 " ideal model delta sigma weight residual 116.30 123.84 -7.54 3.50e+00 8.16e-02 4.64e+00 ... (remaining 3660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.04: 1248 14.04 - 28.07: 177 28.07 - 42.11: 68 42.11 - 56.14: 22 56.14 - 70.18: 5 Dihedral angle restraints: 1520 sinusoidal: 498 harmonic: 1022 Sorted by residual: dihedral pdb=" CA LYS A 67 " pdb=" C LYS A 67 " pdb=" N LYS A 68 " pdb=" CA LYS A 68 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA LYS A 64 " pdb=" C LYS A 64 " pdb=" N LEU A 65 " pdb=" CA LEU A 65 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ARG A 98 " pdb=" CB ARG A 98 " pdb=" CG ARG A 98 " pdb=" CD ARG A 98 " ideal model delta sinusoidal sigma weight residual -60.00 -119.91 59.91 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 269 0.025 - 0.050: 90 0.050 - 0.075: 50 0.075 - 0.100: 27 0.100 - 0.125: 4 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA PRO A 344 " pdb=" N PRO A 344 " pdb=" C PRO A 344 " pdb=" CB PRO A 344 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA PRO A 237 " pdb=" N PRO A 237 " pdb=" C PRO A 237 " pdb=" CB PRO A 237 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.87e-01 chirality pdb=" CA PRO A 144 " pdb=" N PRO A 144 " pdb=" C PRO A 144 " pdb=" CB PRO A 144 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.65e-01 ... (remaining 437 not shown) Planarity restraints: 448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 212 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C LEU A 212 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 212 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 213 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 343 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO A 344 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 211 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.95e+00 pdb=" C THR A 211 " 0.024 2.00e-02 2.50e+03 pdb=" O THR A 211 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 212 " -0.008 2.00e-02 2.50e+03 ... (remaining 445 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 810 2.82 - 3.34: 2787 3.34 - 3.86: 4536 3.86 - 4.38: 4895 4.38 - 4.90: 8587 Nonbonded interactions: 21615 Sorted by model distance: nonbonded pdb=" O LEU A 30 " pdb=" N LEU A 35 " model vdw 2.295 3.120 nonbonded pdb=" OD1 ASN A 137 " pdb=" NE ARG A 310 " model vdw 2.306 3.120 nonbonded pdb=" O GLY A 101 " pdb=" OG SER A 104 " model vdw 2.314 3.040 nonbonded pdb=" O ILE A 295 " pdb=" OG SER A 299 " model vdw 2.359 3.040 nonbonded pdb=" O ALA A 321 " pdb=" NE2 GLN A 325 " model vdw 2.368 3.120 ... (remaining 21610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.360 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.230 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 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 : 0.003 0.030 2694 Z= 0.224 Angle : 0.604 8.907 3665 Z= 0.299 Chirality : 0.038 0.125 440 Planarity : 0.004 0.038 448 Dihedral : 16.770 70.178 868 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 34.14 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.46), residues: 355 helix: 1.93 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -3.86 (0.78), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.002 0.000 HIS A 379 PHE 0.014 0.001 PHE A 47 TYR 0.007 0.001 TYR A 292 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.258 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1091 time to fit residues: 7.6533 Evaluate side-chains 56 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.138553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.112877 restraints weight = 3986.923| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.87 r_work: 0.3259 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2694 Z= 0.264 Angle : 0.572 8.121 3665 Z= 0.287 Chirality : 0.038 0.130 440 Planarity : 0.004 0.039 448 Dihedral : 3.793 17.530 374 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.41 % Allowed : 32.13 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.46), residues: 355 helix: 2.05 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.70 (0.93), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.002 0.001 HIS A 379 PHE 0.014 0.002 PHE A 47 TYR 0.009 0.001 TYR A 278 ARG 0.002 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.288 Fit side-chains REVERT: A 324 ARG cc_start: 0.6987 (mmt180) cc_final: 0.6679 (mtp85) outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 0.1023 time to fit residues: 8.5362 Evaluate side-chains 61 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.139143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114180 restraints weight = 3986.947| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.77 r_work: 0.3276 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2694 Z= 0.242 Angle : 0.554 8.042 3665 Z= 0.275 Chirality : 0.038 0.128 440 Planarity : 0.004 0.038 448 Dihedral : 3.810 17.714 374 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.42 % Allowed : 29.72 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.46), residues: 355 helix: 2.11 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.60 (0.94), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.002 0.000 HIS A 379 PHE 0.013 0.001 PHE A 47 TYR 0.013 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.298 Fit side-chains REVERT: A 8 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8378 (mp) REVERT: A 266 PHE cc_start: 0.7645 (m-10) cc_final: 0.7407 (m-80) REVERT: A 324 ARG cc_start: 0.7048 (mmt180) cc_final: 0.6700 (mtp85) outliers start: 11 outliers final: 4 residues processed: 66 average time/residue: 0.1090 time to fit residues: 9.2254 Evaluate side-chains 62 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.137838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113082 restraints weight = 4000.434| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.78 r_work: 0.3216 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2694 Z= 0.271 Angle : 0.572 7.904 3665 Z= 0.282 Chirality : 0.039 0.143 440 Planarity : 0.004 0.037 448 Dihedral : 3.835 17.581 374 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.02 % Allowed : 31.33 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.46), residues: 355 helix: 2.10 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.60 (0.96), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.002 0.001 HIS A 379 PHE 0.014 0.001 PHE A 47 TYR 0.011 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.289 Fit side-chains REVERT: A 8 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8380 (mp) REVERT: A 65 LEU cc_start: 0.6492 (mp) cc_final: 0.6184 (tt) REVERT: A 324 ARG cc_start: 0.7134 (mmt180) cc_final: 0.6787 (mtp85) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.1055 time to fit residues: 8.9731 Evaluate side-chains 65 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.0000 chunk 14 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.141376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117382 restraints weight = 3953.074| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.81 r_work: 0.3351 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2694 Z= 0.227 Angle : 0.553 7.639 3665 Z= 0.273 Chirality : 0.038 0.149 440 Planarity : 0.004 0.036 448 Dihedral : 3.779 17.477 374 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.42 % Allowed : 31.73 % Favored : 63.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.46), residues: 355 helix: 2.18 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.52 (0.97), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 PHE 0.015 0.001 PHE A 327 TYR 0.016 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.300 Fit side-chains REVERT: A 324 ARG cc_start: 0.7123 (mmt180) cc_final: 0.6753 (mtp85) outliers start: 11 outliers final: 7 residues processed: 66 average time/residue: 0.1116 time to fit residues: 9.4038 Evaluate side-chains 63 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.0770 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.141736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117938 restraints weight = 4028.317| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.83 r_work: 0.3358 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2694 Z= 0.210 Angle : 0.549 7.451 3665 Z= 0.269 Chirality : 0.038 0.154 440 Planarity : 0.004 0.036 448 Dihedral : 3.736 17.376 374 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.02 % Allowed : 30.92 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.46), residues: 355 helix: 2.20 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.61 (0.96), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 PHE 0.016 0.001 PHE A 170 TYR 0.011 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.274 Fit side-chains REVERT: A 324 ARG cc_start: 0.7061 (mmt180) cc_final: 0.6713 (mtp85) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.1044 time to fit residues: 8.8040 Evaluate side-chains 62 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.3132 > 50: distance: 116 - 135: 6.610 distance: 122 - 143: 13.875 distance: 126 - 151: 20.972 distance: 129 - 135: 4.928 distance: 130 - 159: 4.013 distance: 136 - 137: 6.710 distance: 136 - 139: 6.691 distance: 137 - 138: 3.915 distance: 139 - 140: 3.758 distance: 140 - 142: 3.192 distance: 143 - 144: 4.000 distance: 144 - 145: 9.593 distance: 144 - 147: 4.981 distance: 145 - 146: 25.396 distance: 145 - 151: 29.352 distance: 147 - 148: 5.418 distance: 148 - 149: 5.522 distance: 149 - 150: 8.720 distance: 151 - 152: 18.218 distance: 152 - 153: 4.027 distance: 152 - 155: 11.385 distance: 153 - 154: 4.656 distance: 155 - 156: 29.434 distance: 155 - 157: 20.498 distance: 156 - 158: 15.214 distance: 160 - 161: 5.151 distance: 160 - 163: 4.705 distance: 161 - 162: 3.354 distance: 161 - 170: 4.432 distance: 162 - 190: 13.825 distance: 163 - 164: 4.618 distance: 164 - 165: 4.284 distance: 165 - 166: 3.147 distance: 166 - 167: 3.346 distance: 167 - 168: 4.876 distance: 167 - 169: 3.743 distance: 170 - 171: 3.262 distance: 170 - 176: 4.713 distance: 172 - 173: 5.426 distance: 173 - 197: 4.366 distance: 174 - 175: 4.661 distance: 175 - 176: 3.004 distance: 177 - 178: 5.916 distance: 178 - 181: 6.492 distance: 179 - 182: 5.230 distance: 184 - 190: 5.555 distance: 185 - 217: 6.930 distance: 186 - 187: 5.234 distance: 186 - 188: 4.888 distance: 187 - 189: 5.553 distance: 190 - 191: 3.038 distance: 191 - 194: 4.664 distance: 192 - 193: 4.573 distance: 192 - 197: 3.467 distance: 193 - 226: 4.829 distance: 194 - 195: 4.092 distance: 194 - 196: 5.944 distance: 197 - 198: 4.549 distance: 198 - 199: 5.385 distance: 198 - 201: 3.409 distance: 199 - 205: 5.741 distance: 200 - 232: 6.424 distance: 201 - 202: 6.118 distance: 202 - 203: 3.727 distance: 202 - 204: 9.125 distance: 205 - 206: 4.452 distance: 206 - 207: 3.265 distance: 206 - 209: 3.083 distance: 207 - 208: 3.828 distance: 208 - 236: 3.102 distance: 209 - 210: 4.085