Starting phenix.real_space_refine on Thu Jun 5 08:32:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dis_46917/06_2025/9dis_46917.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dis_46917/06_2025/9dis_46917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dis_46917/06_2025/9dis_46917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dis_46917/06_2025/9dis_46917.map" model { file = "/net/cci-nas-00/data/ceres_data/9dis_46917/06_2025/9dis_46917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dis_46917/06_2025/9dis_46917.cif" } resolution = 2.51 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= 0.002 sd= 0.128 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 3570 2.51 5 N 990 2.21 5 O 1146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5721 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 848 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "B" Number of atoms: 4873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4873 Classifications: {'peptide': 627} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 602} Chain breaks: 1 Time building chain proxies: 4.08, per 1000 atoms: 0.71 Number of scatterers: 5721 At special positions: 0 Unit cell: (105.04, 72.72, 73.73, 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 1146 8.00 N 990 7.00 C 3570 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: 1.34 Conformation dependent library (CDL) restraints added in 1.0 seconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 5 sheets defined 19.2% alpha, 47.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 1 through 27 removed outlier: 3.587A pdb=" N GLU A 5 " --> pdb=" O ALA A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 48 Processing helix chain 'A' and resid 48 through 67 Processing helix chain 'A' and resid 69 through 90 removed outlier: 4.698A pdb=" N ALA A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 418 through 424 Processing helix chain 'B' and resid 599 through 603 Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 34 removed outlier: 4.226A pdb=" N MET B 29 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 80 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TYR B 130 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 82 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N THR B 132 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 58 Processing sheet with id=AA4, first strand: chain 'B' and resid 427 through 431 removed outlier: 6.066A pdb=" N LYS B 427 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N TRP B 439 " --> pdb=" O LYS B 427 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N THR B 497 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR B 438 " --> pdb=" O THR B 497 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N SER B 499 " --> pdb=" O TYR B 438 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N THR B 530 " --> pdb=" O PRO B 546 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE B 364 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER B 379 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 10.201A pdb=" N TRP B 390 " --> pdb=" O PHE B 414 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHE B 414 " --> pdb=" O TRP B 390 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 392 " --> pdb=" O GLN B 412 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 471 " --> pdb=" O TYR B 516 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR B 516 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE B 473 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR B 514 " --> pdb=" O PHE B 473 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA B 475 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 512 " --> pdb=" O ALA B 475 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR B 477 " --> pdb=" O TRP B 510 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP B 510 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASP B 479 " --> pdb=" O TRP B 508 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP B 508 " --> pdb=" O ASP B 479 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS B 481 " --> pdb=" O LYS B 506 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS B 506 " --> pdb=" O LYS B 481 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS B 483 " --> pdb=" O ASN B 504 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN B 504 " --> pdb=" O LYS B 483 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 188 376 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 1.62 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: 1937 1.34 - 1.46: 1152 1.46 - 1.57: 2726 1.57 - 1.69: 0 1.69 - 1.80: 30 Bond restraints: 5845 Sorted by residual: bond pdb=" CA ALA A 68 " pdb=" C ALA A 68 " ideal model delta sigma weight residual 1.527 1.516 0.011 1.31e-02 5.83e+03 6.76e-01 bond pdb=" CB TRP B 510 " pdb=" CG TRP B 510 " ideal model delta sigma weight residual 1.498 1.473 0.025 3.10e-02 1.04e+03 6.61e-01 bond pdb=" C LEU B 366 " pdb=" N LEU B 367 " ideal model delta sigma weight residual 1.333 1.324 0.009 1.30e-02 5.92e+03 4.94e-01 bond pdb=" CA SER B 350 " pdb=" CB SER B 350 " ideal model delta sigma weight residual 1.536 1.519 0.017 2.53e-02 1.56e+03 4.52e-01 bond pdb=" CB ASP B 274 " pdb=" CG ASP B 274 " ideal model delta sigma weight residual 1.516 1.499 0.017 2.50e-02 1.60e+03 4.42e-01 ... (remaining 5840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 7621 1.27 - 2.55: 264 2.55 - 3.82: 44 3.82 - 5.09: 7 5.09 - 6.36: 1 Bond angle restraints: 7937 Sorted by residual: angle pdb=" CB ASP B 242 " pdb=" CG ASP B 242 " pdb=" OD2 ASP B 242 " ideal model delta sigma weight residual 118.40 122.97 -4.57 2.30e+00 1.89e-01 3.95e+00 angle pdb=" CA GLY B 97 " pdb=" C GLY B 97 " pdb=" N THR B 98 " ideal model delta sigma weight residual 114.86 116.85 -1.99 1.01e+00 9.80e-01 3.90e+00 angle pdb=" N ASP B 157 " pdb=" CA ASP B 157 " pdb=" C ASP B 157 " ideal model delta sigma weight residual 114.12 111.54 2.58 1.39e+00 5.18e-01 3.44e+00 angle pdb=" OD1 ASP B 242 " pdb=" CG ASP B 242 " pdb=" OD2 ASP B 242 " ideal model delta sigma weight residual 122.90 118.51 4.39 2.40e+00 1.74e-01 3.35e+00 angle pdb=" CA LEU A 105 " pdb=" CB LEU A 105 " pdb=" CG LEU A 105 " ideal model delta sigma weight residual 116.30 122.66 -6.36 3.50e+00 8.16e-02 3.30e+00 ... (remaining 7932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 3190 17.04 - 34.07: 216 34.07 - 51.11: 39 51.11 - 68.14: 9 68.14 - 85.18: 8 Dihedral angle restraints: 3462 sinusoidal: 1333 harmonic: 2129 Sorted by residual: dihedral pdb=" CA ASN B 528 " pdb=" C ASN B 528 " pdb=" N ARG B 529 " pdb=" CA ARG B 529 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA B 229 " pdb=" C ALA B 229 " pdb=" N ARG B 230 " pdb=" CA ARG B 230 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA MET B 422 " pdb=" C MET B 422 " pdb=" N TYR B 423 " pdb=" CA TYR B 423 " ideal model delta harmonic sigma weight residual -180.00 -162.16 -17.84 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 3459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 509 0.032 - 0.064: 235 0.064 - 0.095: 69 0.095 - 0.127: 40 0.127 - 0.159: 3 Chirality restraints: 856 Sorted by residual: chirality pdb=" CB THR B 322 " pdb=" CA THR B 322 " pdb=" OG1 THR B 322 " pdb=" CG2 THR B 322 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CG LEU B 445 " pdb=" CB LEU B 445 " pdb=" CD1 LEU B 445 " pdb=" CD2 LEU B 445 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE B 507 " pdb=" N ILE B 507 " pdb=" C ILE B 507 " pdb=" CB ILE B 507 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 853 not shown) Planarity restraints: 1051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 80 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C ALA A 80 " -0.032 2.00e-02 2.50e+03 pdb=" O ALA A 80 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR A 81 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 79 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C TYR A 79 " -0.030 2.00e-02 2.50e+03 pdb=" O TYR A 79 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 80 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 279 " -0.012 2.00e-02 2.50e+03 1.09e-02 2.99e+00 pdb=" CG TRP B 279 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 279 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 279 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 279 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 279 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 279 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 279 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 279 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 279 " -0.004 2.00e-02 2.50e+03 ... (remaining 1048 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 347 2.73 - 3.27: 5656 3.27 - 3.82: 10037 3.82 - 4.36: 12416 4.36 - 4.90: 21246 Nonbonded interactions: 49702 Sorted by model distance: nonbonded pdb=" OD1 ASP B 511 " pdb=" ND2 ASN B 528 " model vdw 2.190 3.120 nonbonded pdb=" OG SER B 241 " pdb=" OG SER B 244 " model vdw 2.199 3.040 nonbonded pdb=" OD2 ASP B 213 " pdb=" NE2 GLN B 216 " model vdw 2.208 3.120 nonbonded pdb=" OG1 THR B 47 " pdb=" OE1 GLN B 67 " model vdw 2.213 3.040 nonbonded pdb=" NH1 ARG B 230 " pdb=" OD1 ASP B 249 " model vdw 2.233 3.120 ... (remaining 49697 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.990 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:16.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 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 0.025 5845 Z= 0.173 Angle : 0.558 6.362 7937 Z= 0.312 Chirality : 0.043 0.159 856 Planarity : 0.004 0.039 1051 Dihedral : 12.977 85.177 2106 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 0.26 (0.30), residues: 735 helix: 1.51 (0.45), residues: 117 sheet: -0.10 (0.27), residues: 342 loop : 0.19 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 279 HIS 0.002 0.000 HIS B 319 PHE 0.011 0.002 PHE B 434 TYR 0.017 0.001 TYR B 527 ARG 0.006 0.001 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.09921 ( 376) hydrogen bonds : angle 6.46291 ( 1071) covalent geometry : bond 0.00350 ( 5845) covalent geometry : angle 0.55837 ( 7937) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.656 Fit side-chains REVERT: A 34 MET cc_start: 0.6485 (mmp) cc_final: 0.6081 (mmp) REVERT: B 35 THR cc_start: 0.7405 (m) cc_final: 0.7047 (p) REVERT: B 59 ASP cc_start: 0.7795 (m-30) cc_final: 0.7541 (m-30) REVERT: B 204 MET cc_start: 0.8264 (mpp) cc_final: 0.8041 (mpt) REVERT: B 285 ASN cc_start: 0.7141 (t0) cc_final: 0.6877 (t0) REVERT: B 322 THR cc_start: 0.8481 (t) cc_final: 0.8259 (p) REVERT: B 483 LYS cc_start: 0.7579 (tttp) cc_final: 0.7009 (mmtt) outliers start: 0 outliers final: 1 residues processed: 145 average time/residue: 1.4854 time to fit residues: 223.2372 Evaluate side-chains 86 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN B 203 ASN B 216 GLN B 272 ASN B 627 GLN B 631 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.146787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120406 restraints weight = 5669.397| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.50 r_work: 0.3301 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5845 Z= 0.211 Angle : 0.573 5.388 7937 Z= 0.311 Chirality : 0.044 0.142 856 Planarity : 0.004 0.031 1051 Dihedral : 5.163 30.141 817 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.37 % Allowed : 10.94 % Favored : 85.69 % 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: 0.56 (0.31), residues: 735 helix: 2.01 (0.43), residues: 117 sheet: 0.06 (0.27), residues: 343 loop : 0.29 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 510 HIS 0.003 0.001 HIS A 20 PHE 0.014 0.002 PHE B 414 TYR 0.015 0.002 TYR A 81 ARG 0.005 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 376) hydrogen bonds : angle 6.05224 ( 1071) covalent geometry : bond 0.00436 ( 5845) covalent geometry : angle 0.57332 ( 7937) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.580 Fit side-chains REVERT: A 7 LYS cc_start: 0.7143 (tptp) cc_final: 0.6719 (ttpp) REVERT: A 34 MET cc_start: 0.5695 (mmp) cc_final: 0.5248 (mmp) REVERT: A 50 LEU cc_start: 0.7042 (mt) cc_final: 0.6839 (mm) REVERT: B 35 THR cc_start: 0.7770 (m) cc_final: 0.7385 (p) REVERT: B 188 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6824 (mtt90) REVERT: B 274 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7961 (m-30) REVERT: B 281 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: B 285 ASN cc_start: 0.7618 (t0) cc_final: 0.7391 (t0) REVERT: B 356 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7938 (mt-10) REVERT: B 405 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8620 (tmt) REVERT: B 481 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8083 (mtmm) REVERT: B 483 LYS cc_start: 0.8245 (tttp) cc_final: 0.7685 (mmtt) REVERT: B 511 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: B 515 LYS cc_start: 0.8023 (tptp) cc_final: 0.6505 (ttpp) REVERT: B 517 THR cc_start: 0.8691 (t) cc_final: 0.8454 (m) REVERT: B 524 ASP cc_start: 0.8109 (m-30) cc_final: 0.7885 (m-30) outliers start: 20 outliers final: 5 residues processed: 90 average time/residue: 1.4574 time to fit residues: 136.2058 Evaluate side-chains 80 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 333 HIS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 597 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 28 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN B 258 GLN B 268 ASN B 354 GLN B 631 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116241 restraints weight = 5894.430| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.44 r_work: 0.3266 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5845 Z= 0.235 Angle : 0.568 5.887 7937 Z= 0.308 Chirality : 0.042 0.138 856 Planarity : 0.004 0.028 1051 Dihedral : 5.289 31.847 817 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.04 % Allowed : 13.97 % Favored : 81.99 % 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: 0.50 (0.30), residues: 735 helix: 1.90 (0.45), residues: 117 sheet: 0.04 (0.27), residues: 343 loop : 0.24 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 279 HIS 0.003 0.001 HIS B 333 PHE 0.014 0.002 PHE B 407 TYR 0.015 0.002 TYR B 328 ARG 0.004 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 376) hydrogen bonds : angle 6.01287 ( 1071) covalent geometry : bond 0.00479 ( 5845) covalent geometry : angle 0.56795 ( 7937) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.624 Fit side-chains REVERT: A 7 LYS cc_start: 0.7364 (tptp) cc_final: 0.6946 (ttpp) REVERT: A 34 MET cc_start: 0.5690 (mmp) cc_final: 0.5216 (mmp) REVERT: B 35 THR cc_start: 0.7933 (m) cc_final: 0.7573 (p) REVERT: B 51 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7210 (mmp80) REVERT: B 171 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6669 (pp20) REVERT: B 188 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6824 (mtt90) REVERT: B 274 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: B 285 ASN cc_start: 0.7741 (t0) cc_final: 0.7532 (t0) REVERT: B 333 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.6852 (m-70) REVERT: B 405 MET cc_start: 0.8893 (tmt) cc_final: 0.8581 (tmt) REVERT: B 483 LYS cc_start: 0.8390 (tttp) cc_final: 0.7770 (mmtt) REVERT: B 517 THR cc_start: 0.8723 (t) cc_final: 0.8442 (m) REVERT: B 573 ARG cc_start: 0.7326 (mmt180) cc_final: 0.5620 (ptm160) outliers start: 24 outliers final: 10 residues processed: 87 average time/residue: 1.6167 time to fit residues: 145.8400 Evaluate side-chains 80 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 333 HIS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 597 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 0.0040 chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN B 268 ASN B 298 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.146345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119653 restraints weight = 5785.302| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.51 r_work: 0.3288 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5845 Z= 0.162 Angle : 0.519 5.246 7937 Z= 0.280 Chirality : 0.042 0.128 856 Planarity : 0.003 0.028 1051 Dihedral : 4.827 18.709 815 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.21 % Allowed : 15.15 % Favored : 80.64 % 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: 0.41 (0.31), residues: 735 helix: 1.97 (0.45), residues: 117 sheet: -0.07 (0.27), residues: 342 loop : 0.21 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 279 HIS 0.003 0.001 HIS B 333 PHE 0.013 0.002 PHE B 348 TYR 0.012 0.001 TYR B 328 ARG 0.003 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 376) hydrogen bonds : angle 5.88534 ( 1071) covalent geometry : bond 0.00322 ( 5845) covalent geometry : angle 0.51854 ( 7937) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.702 Fit side-chains REVERT: A 7 LYS cc_start: 0.7371 (tptp) cc_final: 0.6939 (ttpp) REVERT: A 34 MET cc_start: 0.5565 (mmp) cc_final: 0.5186 (mmp) REVERT: A 94 GLU cc_start: 0.6497 (mp0) cc_final: 0.6199 (mp0) REVERT: B 35 THR cc_start: 0.7800 (m) cc_final: 0.7443 (p) REVERT: B 51 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7196 (mmp80) REVERT: B 138 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8395 (mt) REVERT: B 188 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6801 (mtt90) REVERT: B 207 LYS cc_start: 0.8659 (tttt) cc_final: 0.8442 (tttm) REVERT: B 274 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7943 (m-30) REVERT: B 281 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: B 285 ASN cc_start: 0.7716 (t0) cc_final: 0.7456 (t0) REVERT: B 329 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7890 (ttm110) REVERT: B 333 HIS cc_start: 0.7400 (OUTLIER) cc_final: 0.6839 (m-70) REVERT: B 339 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7408 (p) REVERT: B 481 LYS cc_start: 0.8873 (mtpt) cc_final: 0.8080 (mtmm) REVERT: B 483 LYS cc_start: 0.8336 (tttp) cc_final: 0.7673 (mmtt) REVERT: B 517 THR cc_start: 0.8631 (t) cc_final: 0.8412 (m) REVERT: B 573 ARG cc_start: 0.7284 (mmt180) cc_final: 0.5521 (ptm160) outliers start: 25 outliers final: 7 residues processed: 85 average time/residue: 1.5120 time to fit residues: 134.0017 Evaluate side-chains 82 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 333 HIS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 597 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 70.4228 > 50: distance: 28 - 148: 10.960 distance: 31 - 145: 17.781 distance: 41 - 137: 5.992 distance: 44 - 134: 7.981 distance: 55 - 128: 12.678 distance: 58 - 125: 4.524 distance: 70 - 116: 33.426 distance: 73 - 113: 35.237 distance: 81 - 102: 24.541 distance: 84 - 99: 5.218 distance: 95 - 99: 3.476 distance: 99 - 100: 8.708 distance: 100 - 101: 10.274 distance: 100 - 103: 12.433 distance: 101 - 102: 17.207 distance: 101 - 105: 5.628 distance: 103 - 104: 6.511 distance: 105 - 106: 12.477 distance: 105 - 229: 6.620 distance: 106 - 107: 24.970 distance: 106 - 109: 24.660 distance: 107 - 108: 31.247 distance: 107 - 113: 6.024 distance: 108 - 226: 5.876 distance: 109 - 110: 21.436 distance: 110 - 111: 18.977 distance: 110 - 112: 9.879 distance: 114 - 115: 48.160 distance: 115 - 116: 25.121 distance: 115 - 117: 15.955 distance: 117 - 118: 17.821 distance: 117 - 217: 10.980 distance: 118 - 119: 17.251 distance: 118 - 121: 23.431 distance: 119 - 120: 20.867 distance: 119 - 125: 7.537 distance: 120 - 214: 20.349 distance: 122 - 124: 40.913 distance: 125 - 126: 15.385 distance: 126 - 127: 10.388 distance: 127 - 128: 15.379 distance: 127 - 129: 14.244 distance: 129 - 201: 10.786 distance: 130 - 131: 4.627 distance: 130 - 133: 9.827 distance: 131 - 132: 3.146 distance: 131 - 134: 6.962 distance: 132 - 198: 11.044 distance: 134 - 135: 4.275 distance: 135 - 136: 6.379 distance: 135 - 138: 7.034 distance: 136 - 137: 11.334 distance: 136 - 140: 20.138 distance: 138 - 139: 9.345 distance: 140 - 190: 15.255 distance: 141 - 142: 8.606 distance: 141 - 144: 6.362 distance: 142 - 143: 13.838 distance: 142 - 145: 12.891 distance: 143 - 187: 17.218 distance: 145 - 146: 5.294 distance: 146 - 147: 12.546 distance: 146 - 149: 16.163 distance: 147 - 148: 16.122 distance: 149 - 150: 9.611 distance: 150 - 151: 20.168 distance: 150 - 152: 11.168 distance: 151 - 153: 8.325 distance: 152 - 154: 16.449 distance: 153 - 155: 7.812 distance: 154 - 155: 3.669 distance: 156 - 157: 16.066 distance: 156 - 179: 10.354 distance: 157 - 158: 15.583 distance: 158 - 159: 9.859 distance: 158 - 160: 24.922 distance: 159 - 176: 32.250