Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 6 22:44:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/10_2023/7p13_13154.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/10_2023/7p13_13154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/10_2023/7p13_13154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/10_2023/7p13_13154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/10_2023/7p13_13154.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/10_2023/7p13_13154.pdb" } resolution = 2.29 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= 0.268 sd= 0.983 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: 5 Type Number sf(0) Gaussians S 49 5.16 5 C 8463 2.51 5 N 2408 2.21 5 O 2653 1.98 5 H 154 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 13727 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Chain: "B" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Chain: "C" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Chain: "D" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Chain: "E" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Chain: "F" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Chain: "G" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Time building chain proxies: 7.50, per 1000 atoms: 0.55 Number of scatterers: 13727 At special positions: 0 Unit cell: (115.092, 113.424, 102.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 O 2653 8.00 N 2408 7.00 C 8463 6.00 H 154 1.00 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 - 3.50 Amino acid : False - 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: 5.28 Conformation dependent library (CDL) restraints added in 1.9 seconds 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 71.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 79 Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 146 through 166 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 179 through 223 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 242 through 268 Proline residue: A 248 - end of helix Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 79 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 146 through 166 Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 179 through 223 Processing helix chain 'B' and resid 225 through 235 Processing helix chain 'B' and resid 242 through 268 Proline residue: B 248 - end of helix Processing helix chain 'C' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 79 Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 146 through 166 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 179 through 223 Processing helix chain 'C' and resid 225 through 235 Processing helix chain 'C' and resid 242 through 268 Proline residue: C 248 - end of helix Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 79 Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 146 through 166 Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 179 through 223 Processing helix chain 'D' and resid 225 through 235 Processing helix chain 'D' and resid 242 through 268 Proline residue: D 248 - end of helix Processing helix chain 'E' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 79 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 146 through 166 Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 179 through 223 Processing helix chain 'E' and resid 225 through 235 Processing helix chain 'E' and resid 242 through 268 Proline residue: E 248 - end of helix Processing helix chain 'F' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 79 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 130 through 142 Processing helix chain 'F' and resid 146 through 166 Processing helix chain 'F' and resid 167 through 171 Processing helix chain 'F' and resid 179 through 223 Processing helix chain 'F' and resid 225 through 235 Processing helix chain 'F' and resid 242 through 268 Proline residue: F 248 - end of helix Processing helix chain 'G' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 79 Processing helix chain 'G' and resid 80 through 82 No H-bonds generated for 'chain 'G' and resid 80 through 82' Processing helix chain 'G' and resid 130 through 142 Processing helix chain 'G' and resid 146 through 166 Processing helix chain 'G' and resid 167 through 171 Processing helix chain 'G' and resid 179 through 223 Processing helix chain 'G' and resid 225 through 235 Processing helix chain 'G' and resid 242 through 268 Proline residue: G 248 - end of helix 987 hydrogen bonds defined for protein. 2919 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: 3.59 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 154 1.02 - 1.21: 49 1.21 - 1.41: 5677 1.41 - 1.60: 8043 1.60 - 1.80: 84 Bond restraints: 14007 Sorted by residual: bond pdb=" C LEU G 270 " pdb=" N GLU G 271 " ideal model delta sigma weight residual 1.329 1.272 0.056 1.60e-02 3.91e+03 1.24e+01 bond pdb=" C LEU E 270 " pdb=" N GLU E 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.23e+01 bond pdb=" C LEU F 270 " pdb=" N GLU F 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.22e+01 bond pdb=" C LEU C 270 " pdb=" N GLU C 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.21e+01 bond pdb=" C LEU B 270 " pdb=" N GLU B 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.21e+01 ... (remaining 14002 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.72: 424 105.72 - 112.79: 7627 112.79 - 119.85: 4861 119.85 - 126.92: 6106 126.92 - 133.99: 183 Bond angle restraints: 19201 Sorted by residual: angle pdb=" C GLU D 258 " pdb=" N LYS D 259 " pdb=" CA LYS D 259 " ideal model delta sigma weight residual 121.14 115.49 5.65 1.75e+00 3.27e-01 1.04e+01 angle pdb=" C GLU E 258 " pdb=" N LYS E 259 " pdb=" CA LYS E 259 " ideal model delta sigma weight residual 121.14 115.50 5.64 1.75e+00 3.27e-01 1.04e+01 angle pdb=" C GLU B 258 " pdb=" N LYS B 259 " pdb=" CA LYS B 259 " ideal model delta sigma weight residual 121.14 115.54 5.60 1.75e+00 3.27e-01 1.02e+01 angle pdb=" C GLU A 258 " pdb=" N LYS A 259 " pdb=" CA LYS A 259 " ideal model delta sigma weight residual 121.14 115.55 5.59 1.75e+00 3.27e-01 1.02e+01 angle pdb=" C GLU G 258 " pdb=" N LYS G 259 " pdb=" CA LYS G 259 " ideal model delta sigma weight residual 121.14 115.56 5.58 1.75e+00 3.27e-01 1.02e+01 ... (remaining 19196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 7468 14.99 - 29.99: 881 29.99 - 44.98: 156 44.98 - 59.97: 21 59.97 - 74.97: 42 Dihedral angle restraints: 8568 sinusoidal: 3437 harmonic: 5131 Sorted by residual: dihedral pdb=" CA PRO C 286 " pdb=" C PRO C 286 " pdb=" N PRO C 287 " pdb=" CA PRO C 287 " ideal model delta harmonic sigma weight residual -180.00 -148.65 -31.35 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA PRO E 286 " pdb=" C PRO E 286 " pdb=" N PRO E 287 " pdb=" CA PRO E 287 " ideal model delta harmonic sigma weight residual -180.00 -148.70 -31.30 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" CA PRO D 286 " pdb=" C PRO D 286 " pdb=" N PRO D 287 " pdb=" CA PRO D 287 " ideal model delta harmonic sigma weight residual -180.00 -148.71 -31.29 0 5.00e+00 4.00e-02 3.92e+01 ... (remaining 8565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1238 0.055 - 0.110: 624 0.110 - 0.165: 161 0.165 - 0.221: 21 0.221 - 0.276: 7 Chirality restraints: 2051 Sorted by residual: chirality pdb=" CA GLU A 222 " pdb=" N GLU A 222 " pdb=" C GLU A 222 " pdb=" CB GLU A 222 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLU E 222 " pdb=" N GLU E 222 " pdb=" C GLU E 222 " pdb=" CB GLU E 222 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLU F 222 " pdb=" N GLU F 222 " pdb=" C GLU F 222 " pdb=" CB GLU F 222 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2048 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 286 " 0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO D 287 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 287 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 287 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 286 " 0.050 5.00e-02 4.00e+02 7.47e-02 8.93e+00 pdb=" N PRO E 287 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO E 287 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 287 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 286 " 0.050 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO A 287 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " 0.037 5.00e-02 4.00e+02 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.60: 422 2.60 - 3.10: 10723 3.10 - 3.60: 17626 3.60 - 4.10: 22963 4.10 - 4.60: 36459 Nonbonded interactions: 88193 Sorted by model distance: nonbonded pdb=" HB THR D 262 " pdb=" HG1 THR D 262 " model vdw 2.103 1.816 nonbonded pdb=" HB THR E 262 " pdb=" HG1 THR E 262 " model vdw 2.105 1.816 nonbonded pdb=" HB THR C 262 " pdb=" HG1 THR C 262 " model vdw 2.105 1.816 nonbonded pdb=" HB THR B 262 " pdb=" HG1 THR B 262 " model vdw 2.119 1.816 nonbonded pdb=" HB2 GLU F 258 " pdb=" HG3 GLU F 258 " model vdw 2.133 1.952 ... (remaining 88188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.940 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: 0.330 Extract box with map and model: 4.160 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 35.970 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.070 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:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.016 0.075 13853 Z= 1.029 Angle : 1.063 11.313 18851 Z= 0.565 Chirality : 0.067 0.276 2051 Planarity : 0.008 0.075 2555 Dihedral : 14.069 74.966 5194 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: 2.06 (0.20), residues: 1715 helix: 1.67 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 0.86 (0.30), residues: 511 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.652 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 1.6980 time to fit residues: 676.9752 Evaluate side-chains 250 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.555 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 ASN A 245 GLN A 254 GLN B 11 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN C 11 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN E 254 GLN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN G 245 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13853 Z= 0.150 Angle : 0.489 7.052 18851 Z= 0.256 Chirality : 0.034 0.120 2051 Planarity : 0.005 0.061 2555 Dihedral : 3.933 13.746 1883 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.80 % Allowed : 11.18 % Favored : 87.01 % 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: 4.36 (0.21), residues: 1715 helix: 3.68 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 0.99 (0.31), residues: 525 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 319 time to evaluate : 1.692 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 334 average time/residue: 1.4256 time to fit residues: 515.5589 Evaluate side-chains 290 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 278 time to evaluate : 1.521 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 1.1977 time to fit residues: 7.2431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 152 optimal weight: 0.1980 chunk 165 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13853 Z= 0.106 Angle : 0.411 6.190 18851 Z= 0.206 Chirality : 0.032 0.152 2051 Planarity : 0.004 0.046 2555 Dihedral : 3.374 11.830 1883 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.16 % Allowed : 12.63 % Favored : 85.21 % 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: 5.07 (0.21), residues: 1715 helix: 4.18 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : 1.15 (0.32), residues: 497 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 307 time to evaluate : 1.633 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 321 average time/residue: 1.4815 time to fit residues: 514.0737 Evaluate side-chains 298 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 283 time to evaluate : 1.452 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 7 residues processed: 8 average time/residue: 0.4770 time to fit residues: 6.5718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN F 48 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13853 Z= 0.303 Angle : 0.529 5.298 18851 Z= 0.277 Chirality : 0.038 0.115 2051 Planarity : 0.005 0.057 2555 Dihedral : 3.688 13.093 1883 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.10 % Allowed : 13.06 % Favored : 83.84 % 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: 4.55 (0.21), residues: 1715 helix: 3.69 (0.14), residues: 1232 sheet: None (None), residues: 0 loop : 1.16 (0.32), residues: 483 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 265 time to evaluate : 1.601 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 23 residues processed: 290 average time/residue: 1.5071 time to fit residues: 471.5805 Evaluate side-chains 285 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 262 time to evaluate : 1.525 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 16 residues processed: 7 average time/residue: 0.8346 time to fit residues: 8.8522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 120 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 13853 Z= 0.273 Angle : 0.511 5.451 18851 Z= 0.267 Chirality : 0.037 0.116 2051 Planarity : 0.005 0.055 2555 Dihedral : 3.693 13.222 1883 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.61 % Allowed : 14.07 % Favored : 82.32 % 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: 4.69 (0.21), residues: 1715 helix: 3.88 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.23 (0.32), residues: 525 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 258 time to evaluate : 1.616 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 27 residues processed: 287 average time/residue: 1.4867 time to fit residues: 460.3921 Evaluate side-chains 282 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 255 time to evaluate : 1.449 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 17 residues processed: 10 average time/residue: 0.6061 time to fit residues: 9.2639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 13853 Z= 0.178 Angle : 0.446 4.858 18851 Z= 0.233 Chirality : 0.034 0.120 2051 Planarity : 0.004 0.047 2555 Dihedral : 3.494 11.601 1883 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.17 % Allowed : 15.37 % Favored : 81.46 % 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: 4.72 (0.21), residues: 1715 helix: 3.85 (0.14), residues: 1232 sheet: None (None), residues: 0 loop : 1.14 (0.32), residues: 483 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 272 time to evaluate : 1.527 Fit side-chains outliers start: 44 outliers final: 23 residues processed: 294 average time/residue: 1.5061 time to fit residues: 478.1554 Evaluate side-chains 290 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 267 time to evaluate : 1.684 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 14 residues processed: 9 average time/residue: 0.6426 time to fit residues: 8.9752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.4333 > 50: distance: 42 - 64: 27.035 distance: 46 - 78: 28.607 distance: 51 - 83: 25.117 distance: 59 - 64: 27.990 distance: 60 - 94: 21.876 distance: 64 - 65: 20.725 distance: 65 - 66: 3.057 distance: 65 - 68: 43.109 distance: 66 - 67: 44.744 distance: 66 - 78: 31.172 distance: 67 - 105: 41.445 distance: 68 - 69: 16.219 distance: 69 - 70: 31.489 distance: 69 - 71: 33.012 distance: 70 - 72: 23.915 distance: 71 - 73: 13.482 distance: 71 - 74: 7.160 distance: 72 - 73: 7.523 distance: 73 - 75: 18.869 distance: 74 - 76: 36.404 distance: 75 - 77: 31.122 distance: 76 - 77: 17.834 distance: 78 - 79: 11.821 distance: 79 - 80: 13.256 distance: 79 - 82: 28.042 distance: 80 - 81: 19.004 distance: 80 - 83: 31.468 distance: 81 - 114: 36.078 distance: 83 - 84: 31.038 distance: 84 - 85: 50.791 distance: 84 - 87: 43.723 distance: 85 - 86: 56.424 distance: 85 - 94: 30.158 distance: 87 - 88: 29.807 distance: 88 - 89: 8.381 distance: 89 - 90: 36.698 distance: 90 - 91: 8.530 distance: 91 - 92: 30.903 distance: 91 - 93: 20.913 distance: 94 - 95: 43.818 distance: 95 - 96: 39.982 distance: 95 - 98: 19.738 distance: 96 - 97: 26.706 distance: 96 - 105: 39.965 distance: 98 - 99: 43.954 distance: 99 - 100: 39.146 distance: 100 - 101: 39.803 distance: 101 - 102: 18.262 distance: 102 - 103: 44.636 distance: 102 - 104: 50.068 distance: 105 - 106: 39.655 distance: 106 - 107: 43.314 distance: 106 - 109: 38.790 distance: 107 - 108: 42.803 distance: 107 - 114: 42.573 distance: 110 - 111: 5.465 distance: 111 - 112: 39.153 distance: 111 - 113: 41.236 distance: 114 - 115: 32.278 distance: 115 - 116: 43.513 distance: 115 - 118: 33.326 distance: 116 - 117: 47.443 distance: 116 - 124: 45.932 distance: 119 - 120: 11.231 distance: 119 - 121: 35.530 distance: 120 - 122: 33.741 distance: 121 - 123: 17.062 distance: 122 - 123: 48.707 distance: 124 - 125: 39.516 distance: 124 - 130: 13.629 distance: 125 - 128: 27.743 distance: 126 - 127: 40.329 distance: 126 - 131: 42.804 distance: 128 - 129: 23.224 distance: 129 - 130: 31.407 distance: 131 - 132: 36.064 distance: 132 - 133: 11.259 distance: 132 - 135: 16.002 distance: 133 - 134: 40.644 distance: 133 - 138: 14.490 distance: 134 - 167: 28.362 distance: 135 - 136: 19.893 distance: 135 - 137: 45.886 distance: 138 - 139: 29.833 distance: 139 - 142: 12.250 distance: 140 - 141: 4.384 distance: 140 - 150: 31.206 distance: 141 - 175: 33.400 distance: 142 - 143: 41.209 distance: 143 - 144: 56.550 distance: 143 - 145: 19.836 distance: 144 - 146: 40.448 distance: 145 - 147: 8.758 distance: 146 - 148: 32.440 distance: 147 - 148: 30.105 distance: 148 - 149: 14.542 distance: 150 - 151: 25.459 distance: 151 - 152: 43.993 distance: 152 - 153: 10.881 distance: 152 - 159: 28.764 distance: 153 - 182: 26.866 distance: 154 - 155: 54.811 distance: 155 - 156: 29.310 distance: 156 - 157: 58.407 distance: 156 - 158: 21.079