Starting phenix.real_space_refine on Mon Feb 10 22:48:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ex5_28651/02_2025/8ex5_28651.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ex5_28651/02_2025/8ex5_28651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ex5_28651/02_2025/8ex5_28651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ex5_28651/02_2025/8ex5_28651.map" model { file = "/net/cci-nas-00/data/ceres_data/8ex5_28651/02_2025/8ex5_28651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ex5_28651/02_2025/8ex5_28651.cif" } resolution = 3.47 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= 0.001 sd= 0.018 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 17 5.16 5 C 2090 2.51 5 N 524 2.21 5 O 546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3177 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3177 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 12, 'TRANS': 401} Chain breaks: 2 Time building chain proxies: 4.82, per 1000 atoms: 1.52 Number of scatterers: 3177 At special positions: 0 Unit cell: (70.092, 68.794, 79.827, 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 17 16.00 O 546 8.00 N 524 7.00 C 2090 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: 0.78 Conformation dependent library (CDL) restraints added in 362.5 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 90.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 99 through 134 removed outlier: 3.628A pdb=" N ALA A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASP A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 165 removed outlier: 3.726A pdb=" N ALA A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 3.792A pdb=" N ARG A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 186 Processing helix chain 'A' and resid 193 through 222 Proline residue: A 215 - end of helix removed outlier: 3.820A pdb=" N PHE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 256 removed outlier: 4.259A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 265 through 281 removed outlier: 4.435A pdb=" N LEU A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 281 " --> pdb=" O ILE A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 312 through 348 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 361 through 392 Processing helix chain 'A' and resid 394 through 417 removed outlier: 3.635A pdb=" N LEU A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 438 removed outlier: 4.295A pdb=" N LEU A 435 " --> pdb=" O VAL A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 450 removed outlier: 3.583A pdb=" N ALA A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 455 through 470 Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 493 through 538 removed outlier: 4.238A pdb=" N CYS A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Proline residue: A 509 - end of helix removed outlier: 5.161A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 822 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: 0.91 Time building geometry restraints manager: 0.91 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: 968 1.34 - 1.46: 631 1.46 - 1.58: 1626 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3251 Sorted by residual: bond pdb=" C CYS A 508 " pdb=" N PRO A 509 " ideal model delta sigma weight residual 1.333 1.356 -0.023 1.44e-02 4.82e+03 2.55e+00 bond pdb=" C SER A 266 " pdb=" N PRO A 267 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.14e+00 bond pdb=" N LYS A 224 " pdb=" CA LYS A 224 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 2.00e+00 bond pdb=" CG LEU A 171 " pdb=" CD2 LEU A 171 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.25e+00 bond pdb=" CB ILE A 107 " pdb=" CG2 ILE A 107 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.99e-01 ... (remaining 3246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 4132 1.27 - 2.55: 227 2.55 - 3.82: 35 3.82 - 5.10: 16 5.10 - 6.37: 6 Bond angle restraints: 4416 Sorted by residual: angle pdb=" N ILE A 188 " pdb=" CA ILE A 188 " pdb=" C ILE A 188 " ideal model delta sigma weight residual 108.95 112.36 -3.41 9.80e-01 1.04e+00 1.21e+01 angle pdb=" N VAL A 431 " pdb=" CA VAL A 431 " pdb=" C VAL A 431 " ideal model delta sigma weight residual 112.80 108.88 3.92 1.15e+00 7.56e-01 1.16e+01 angle pdb=" C PHE A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta sigma weight residual 120.31 115.32 4.99 1.52e+00 4.33e-01 1.08e+01 angle pdb=" N TRP A 178 " pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " ideal model delta sigma weight residual 110.28 115.08 -4.80 1.55e+00 4.16e-01 9.58e+00 angle pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " pdb=" CG TRP A 178 " ideal model delta sigma weight residual 113.60 119.39 -5.79 1.90e+00 2.77e-01 9.28e+00 ... (remaining 4411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 1714 15.94 - 31.88: 125 31.88 - 47.82: 26 47.82 - 63.75: 6 63.75 - 79.69: 1 Dihedral angle restraints: 1872 sinusoidal: 692 harmonic: 1180 Sorted by residual: dihedral pdb=" CA THR A 223 " pdb=" C THR A 223 " pdb=" N LYS A 224 " pdb=" CA LYS A 224 " ideal model delta harmonic sigma weight residual 180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLU A 207 " pdb=" C GLU A 207 " pdb=" N ALA A 208 " pdb=" CA ALA A 208 " ideal model delta harmonic sigma weight residual 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LEU A 221 " pdb=" C LEU A 221 " pdb=" N PHE A 222 " pdb=" CA PHE A 222 " ideal model delta harmonic sigma weight residual 180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 1869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 313 0.031 - 0.061: 146 0.061 - 0.092: 39 0.092 - 0.123: 18 0.123 - 0.153: 5 Chirality restraints: 521 Sorted by residual: chirality pdb=" CA GLU A 207 " pdb=" N GLU A 207 " pdb=" C GLU A 207 " pdb=" CB GLU A 207 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA PRO A 267 " pdb=" N PRO A 267 " pdb=" C PRO A 267 " pdb=" CB PRO A 267 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA SER A 475 " pdb=" N SER A 475 " pdb=" C SER A 475 " pdb=" CB SER A 475 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 518 not shown) Planarity restraints: 539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " 0.025 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP A 178 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 508 " -0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO A 509 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 509 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 509 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 223 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C THR A 223 " 0.025 2.00e-02 2.50e+03 pdb=" O THR A 223 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 224 " -0.008 2.00e-02 2.50e+03 ... (remaining 536 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 52 2.69 - 3.24: 3428 3.24 - 3.80: 5240 3.80 - 4.35: 6680 4.35 - 4.90: 11130 Nonbonded interactions: 26530 Sorted by model distance: nonbonded pdb=" OG SER A 186 " pdb=" O LEU A 263 " model vdw 2.141 3.040 nonbonded pdb=" O GLY A 206 " pdb=" OG SER A 209 " model vdw 2.182 3.040 nonbonded pdb=" OD1 ASP A 118 " pdb=" OG SER A 266 " model vdw 2.290 3.040 nonbonded pdb=" O MET A 404 " pdb=" OG SER A 407 " model vdw 2.296 3.040 nonbonded pdb=" NH1 ARG A 167 " pdb=" OG1 THR A 216 " model vdw 2.368 3.120 ... (remaining 26525 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.810 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: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3251 Z= 0.287 Angle : 0.714 6.370 4416 Z= 0.423 Chirality : 0.041 0.153 521 Planarity : 0.005 0.051 539 Dihedral : 12.108 79.692 1116 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.88 (0.42), residues: 408 helix: 1.13 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -2.78 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP A 178 HIS 0.001 0.001 HIS A 260 PHE 0.023 0.002 PHE A 465 TYR 0.018 0.002 TYR A 426 ARG 0.005 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.315 Fit side-chains REVERT: A 182 THR cc_start: 0.7787 (m) cc_final: 0.6251 (t) REVERT: A 447 LEU cc_start: 0.8555 (tt) cc_final: 0.8258 (tp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1307 time to fit residues: 6.7244 Evaluate side-chains 35 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 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 344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.235576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.213862 restraints weight = 3653.241| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 1.52 r_work: 0.4199 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3251 Z= 0.226 Angle : 0.599 6.231 4416 Z= 0.323 Chirality : 0.042 0.154 521 Planarity : 0.004 0.049 539 Dihedral : 4.961 20.893 444 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.30 % Allowed : 6.87 % Favored : 92.84 % 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: 1.43 (0.41), residues: 408 helix: 1.50 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -2.64 (0.77), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 178 HIS 0.002 0.001 HIS A 468 PHE 0.014 0.002 PHE A 327 TYR 0.016 0.002 TYR A 426 ARG 0.004 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.332 Fit side-chains REVERT: A 182 THR cc_start: 0.8039 (m) cc_final: 0.6328 (t) REVERT: A 264 ARG cc_start: 0.4556 (mtp85) cc_final: 0.3547 (mtp-110) REVERT: A 447 LEU cc_start: 0.8585 (tt) cc_final: 0.8308 (tp) outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.1385 time to fit residues: 7.2296 Evaluate side-chains 40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.235452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.213555 restraints weight = 3656.319| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 1.52 r_work: 0.4174 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3251 Z= 0.236 Angle : 0.584 6.295 4416 Z= 0.315 Chirality : 0.042 0.144 521 Planarity : 0.004 0.049 539 Dihedral : 4.859 21.258 444 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.90 % Allowed : 10.15 % Favored : 88.96 % 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: 1.51 (0.41), residues: 408 helix: 1.52 (0.27), residues: 356 sheet: None (None), residues: 0 loop : -2.63 (0.81), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 178 HIS 0.002 0.001 HIS A 468 PHE 0.015 0.002 PHE A 327 TYR 0.015 0.002 TYR A 426 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.297 Fit side-chains REVERT: A 182 THR cc_start: 0.8071 (m) cc_final: 0.6387 (t) REVERT: A 264 ARG cc_start: 0.4533 (mtp85) cc_final: 0.3367 (mtp-110) REVERT: A 447 LEU cc_start: 0.8594 (tt) cc_final: 0.8314 (tp) outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.1376 time to fit residues: 7.5414 Evaluate side-chains 41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.235006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.213107 restraints weight = 3674.457| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 1.53 r_work: 0.4166 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3251 Z= 0.237 Angle : 0.577 6.395 4416 Z= 0.311 Chirality : 0.042 0.142 521 Planarity : 0.004 0.049 539 Dihedral : 4.823 20.868 444 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.19 % Allowed : 11.64 % Favored : 87.16 % 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: 1.62 (0.41), residues: 408 helix: 1.60 (0.27), residues: 356 sheet: None (None), residues: 0 loop : -2.54 (0.81), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 178 HIS 0.002 0.001 HIS A 468 PHE 0.014 0.002 PHE A 327 TYR 0.016 0.002 TYR A 426 ARG 0.004 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.318 Fit side-chains REVERT: A 182 THR cc_start: 0.8083 (m) cc_final: 0.6432 (t) REVERT: A 264 ARG cc_start: 0.4641 (mtp85) cc_final: 0.3256 (mtp-110) REVERT: A 439 ASN cc_start: 0.7383 (p0) cc_final: 0.6645 (m-40) REVERT: A 447 LEU cc_start: 0.8607 (tt) cc_final: 0.8342 (tp) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.1438 time to fit residues: 8.0694 Evaluate side-chains 42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 248 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.234576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.212742 restraints weight = 3640.549| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 1.51 r_work: 0.4164 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3251 Z= 0.239 Angle : 0.580 6.328 4416 Z= 0.311 Chirality : 0.042 0.141 521 Planarity : 0.004 0.049 539 Dihedral : 4.831 21.093 444 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.19 % Allowed : 12.54 % Favored : 86.27 % 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: 1.71 (0.41), residues: 408 helix: 1.63 (0.27), residues: 356 sheet: None (None), residues: 0 loop : -2.35 (0.83), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 178 HIS 0.002 0.001 HIS A 468 PHE 0.014 0.002 PHE A 327 TYR 0.016 0.002 TYR A 426 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.360 Fit side-chains REVERT: A 182 THR cc_start: 0.8100 (m) cc_final: 0.6464 (t) REVERT: A 264 ARG cc_start: 0.4711 (mtp85) cc_final: 0.3172 (mtp-110) REVERT: A 439 ASN cc_start: 0.7303 (p0) cc_final: 0.6718 (m-40) outliers start: 4 outliers final: 4 residues processed: 41 average time/residue: 0.1192 time to fit residues: 6.7774 Evaluate side-chains 44 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 385 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 0.0870 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.236520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.214611 restraints weight = 3714.568| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 1.53 r_work: 0.4177 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3251 Z= 0.204 Angle : 0.551 6.040 4416 Z= 0.295 Chirality : 0.040 0.140 521 Planarity : 0.004 0.049 539 Dihedral : 4.706 20.228 444 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.49 % Allowed : 12.54 % Favored : 85.97 % 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: 1.96 (0.42), residues: 408 helix: 1.80 (0.27), residues: 356 sheet: None (None), residues: 0 loop : -2.28 (0.84), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 178 HIS 0.002 0.001 HIS A 468 PHE 0.013 0.002 PHE A 327 TYR 0.016 0.002 TYR A 426 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.331 Fit side-chains REVERT: A 182 THR cc_start: 0.8063 (m) cc_final: 0.6392 (t) REVERT: A 264 ARG cc_start: 0.4717 (mtp85) cc_final: 0.3304 (mtm110) REVERT: A 439 ASN cc_start: 0.7209 (p0) cc_final: 0.6809 (m-40) REVERT: A 447 LEU cc_start: 0.8582 (tt) cc_final: 0.8301 (tp) outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.1328 time to fit residues: 7.7144 Evaluate side-chains 42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 385 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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: 57.1661 > 50: distance: 106 - 121: 3.538 distance: 114 - 136: 29.111 distance: 118 - 144: 26.615 distance: 123 - 128: 7.388 distance: 124 - 155: 19.832 distance: 128 - 129: 17.302 distance: 129 - 130: 12.120 distance: 129 - 132: 15.372 distance: 130 - 131: 12.364 distance: 130 - 136: 28.111 distance: 132 - 133: 11.119 distance: 133 - 134: 19.007 distance: 133 - 135: 35.205 distance: 136 - 137: 11.166 distance: 137 - 138: 7.965 distance: 137 - 140: 29.639 distance: 138 - 139: 10.616 distance: 138 - 144: 42.362 distance: 140 - 141: 16.570 distance: 141 - 142: 21.161 distance: 141 - 143: 11.041 distance: 144 - 145: 46.063 distance: 145 - 146: 22.060 distance: 145 - 148: 13.391 distance: 146 - 147: 12.018 distance: 146 - 155: 12.102 distance: 148 - 149: 16.000 distance: 149 - 150: 11.524 distance: 149 - 151: 8.170 distance: 150 - 152: 12.423 distance: 151 - 153: 13.520 distance: 152 - 154: 10.309 distance: 153 - 154: 12.967 distance: 155 - 156: 12.943 distance: 156 - 157: 4.498 distance: 156 - 159: 23.076 distance: 157 - 158: 8.746 distance: 157 - 161: 21.402 distance: 159 - 160: 10.610 distance: 161 - 162: 12.050 distance: 162 - 163: 7.803 distance: 162 - 165: 15.486 distance: 163 - 164: 16.642 distance: 163 - 169: 16.236 distance: 165 - 166: 11.762 distance: 166 - 167: 14.780 distance: 166 - 168: 28.491 distance: 169 - 170: 3.978 distance: 170 - 171: 12.901 distance: 170 - 173: 16.079 distance: 171 - 172: 21.765 distance: 171 - 183: 17.421 distance: 173 - 174: 21.700 distance: 174 - 176: 9.756 distance: 175 - 177: 13.267 distance: 176 - 178: 7.045 distance: 176 - 179: 7.296 distance: 177 - 178: 12.551 distance: 178 - 180: 19.413 distance: 179 - 181: 5.733 distance: 180 - 182: 6.513 distance: 181 - 182: 10.455 distance: 183 - 184: 4.679 distance: 184 - 185: 5.672 distance: 184 - 187: 19.545 distance: 185 - 186: 9.935 distance: 185 - 188: 14.563 distance: 186 - 208: 18.080 distance: 188 - 189: 5.383 distance: 189 - 190: 16.824 distance: 189 - 192: 12.138 distance: 190 - 191: 12.687 distance: 190 - 196: 22.369 distance: 191 - 216: 22.166 distance: 192 - 193: 18.019 distance: 192 - 194: 30.932 distance: 193 - 195: 20.410 distance: 196 - 197: 20.663 distance: 197 - 198: 13.658 distance: 197 - 200: 20.956 distance: 198 - 199: 7.410 distance: 198 - 203: 9.282 distance: 199 - 224: 16.089 distance: 200 - 201: 26.293 distance: 200 - 202: 30.451 distance: 203 - 204: 12.129 distance: 204 - 205: 35.132 distance: 204 - 207: 7.478 distance: 205 - 206: 28.198 distance: 205 - 208: 24.790 distance: 206 - 230: 33.079