Starting phenix.real_space_refine on Fri Dec 27 12:21:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b23_44095/12_2024/9b23_44095.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b23_44095/12_2024/9b23_44095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b23_44095/12_2024/9b23_44095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b23_44095/12_2024/9b23_44095.map" model { file = "/net/cci-nas-00/data/ceres_data/9b23_44095/12_2024/9b23_44095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b23_44095/12_2024/9b23_44095.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2975 2.51 5 N 748 2.21 5 O 937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4670 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2342 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain: "E" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2328 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 12, 'TRANS': 270} Time building chain proxies: 3.52, per 1000 atoms: 0.75 Number of scatterers: 4670 At special positions: 0 Unit cell: (69.72, 86.32, 123.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 937 8.00 N 748 7.00 C 2975 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: 1.20 Conformation dependent library (CDL) restraints added in 553.4 milliseconds 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1080 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 4 sheets defined 56.9% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'D' and resid 81 through 88 Processing helix chain 'D' and resid 89 through 141 Proline residue: D 130 - end of helix Processing helix chain 'D' and resid 146 through 159 Processing helix chain 'D' and resid 162 through 166 Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 187 through 196 Processing helix chain 'D' and resid 196 through 201 removed outlier: 4.021A pdb=" N ASP D 201 " --> pdb=" O PRO D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.804A pdb=" N VAL D 210 " --> pdb=" O ARG D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 316 Processing helix chain 'D' and resid 322 through 352 removed outlier: 4.070A pdb=" N GLU D 328 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 338 " --> pdb=" O LEU D 334 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA D 339 " --> pdb=" O GLU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'E' and resid 84 through 88 Processing helix chain 'E' and resid 89 through 140 removed outlier: 3.576A pdb=" N LYS E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Proline residue: E 130 - end of helix Processing helix chain 'E' and resid 146 through 161 Processing helix chain 'E' and resid 162 through 166 removed outlier: 3.543A pdb=" N LEU E 165 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 173 Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'E' and resid 198 through 203 removed outlier: 3.936A pdb=" N THR E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 203' Processing helix chain 'E' and resid 204 through 212 Processing helix chain 'E' and resid 259 through 263 removed outlier: 4.253A pdb=" N ASP E 263 " --> pdb=" O TYR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 316 Processing helix chain 'E' and resid 324 through 326 No H-bonds generated for 'chain 'E' and resid 324 through 326' Processing helix chain 'E' and resid 327 through 351 removed outlier: 4.337A pdb=" N ASP E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 362 Processing sheet with id=AA1, first strand: chain 'D' and resid 216 through 221 removed outlier: 4.429A pdb=" N ASP D 216 " --> pdb=" O ARG D 234 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 234 " --> pdb=" O ASP D 216 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N CYS D 249 " --> pdb=" O GLY D 271 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLY D 271 " --> pdb=" O CYS D 249 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N THR D 251 " --> pdb=" O ALA D 269 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ALA D 269 " --> pdb=" O THR D 251 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE D 253 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 285 through 294 Processing sheet with id=AA3, first strand: chain 'E' and resid 214 through 222 removed outlier: 3.993A pdb=" N GLY E 228 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N CYS E 249 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY E 271 " --> pdb=" O CYS E 249 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR E 251 " --> pdb=" O ALA E 269 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ALA E 269 " --> pdb=" O THR E 251 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE E 253 " --> pdb=" O ASP E 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 285 through 293 removed outlier: 3.533A pdb=" N GLU E 288 " --> pdb=" O LYS E 305 " (cutoff:3.500A) 248 hydrogen bonds defined for protein. 711 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: 1.25 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1451 1.33 - 1.45: 616 1.45 - 1.57: 2683 1.57 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 4764 Sorted by residual: bond pdb=" N THR D 163 " pdb=" CA THR D 163 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.32e+00 bond pdb=" N GLU D 162 " pdb=" CA GLU D 162 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.25e-02 6.40e+03 5.21e+00 bond pdb=" N LEU D 160 " pdb=" CA LEU D 160 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.80e+00 bond pdb=" N LEU D 165 " pdb=" CA LEU D 165 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.33e-02 5.65e+03 4.73e+00 bond pdb=" N GLU D 164 " pdb=" CA GLU D 164 " ideal model delta sigma weight residual 1.458 1.485 -0.026 1.27e-02 6.20e+03 4.25e+00 ... (remaining 4759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 5994 1.04 - 2.08: 337 2.08 - 3.12: 72 3.12 - 4.15: 26 4.15 - 5.19: 4 Bond angle restraints: 6433 Sorted by residual: angle pdb=" C PRO E 308 " pdb=" CA PRO E 308 " pdb=" CB PRO E 308 " ideal model delta sigma weight residual 111.23 107.44 3.79 1.28e+00 6.10e-01 8.76e+00 angle pdb=" N GLU D 164 " pdb=" CA GLU D 164 " pdb=" C GLU D 164 " ideal model delta sigma weight residual 111.75 107.99 3.76 1.28e+00 6.10e-01 8.64e+00 angle pdb=" CA PRO E 308 " pdb=" C PRO E 308 " pdb=" O PRO E 308 " ideal model delta sigma weight residual 121.56 118.19 3.37 1.16e+00 7.43e-01 8.46e+00 angle pdb=" C PHE E 316 " pdb=" N ASP E 317 " pdb=" CA ASP E 317 " ideal model delta sigma weight residual 123.10 120.45 2.65 9.60e-01 1.09e+00 7.65e+00 angle pdb=" CA GLU D 162 " pdb=" C GLU D 162 " pdb=" O GLU D 162 " ideal model delta sigma weight residual 120.32 117.50 2.82 1.02e+00 9.61e-01 7.62e+00 ... (remaining 6428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 2629 17.89 - 35.78: 211 35.78 - 53.67: 44 53.67 - 71.57: 15 71.57 - 89.46: 6 Dihedral angle restraints: 2905 sinusoidal: 1241 harmonic: 1664 Sorted by residual: dihedral pdb=" CA ILE D 265 " pdb=" C ILE D 265 " pdb=" N TYR D 266 " pdb=" CA TYR D 266 " ideal model delta harmonic sigma weight residual 180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA TYR E 266 " pdb=" C TYR E 266 " pdb=" N ASP E 267 " pdb=" CA ASP E 267 " ideal model delta harmonic sigma weight residual 180.00 157.83 22.17 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA GLN D 322 " pdb=" C GLN D 322 " pdb=" N ASN D 323 " pdb=" CA ASN D 323 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 2902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 467 0.031 - 0.062: 136 0.062 - 0.092: 52 0.092 - 0.123: 29 0.123 - 0.154: 6 Chirality restraints: 690 Sorted by residual: chirality pdb=" CA LEU D 160 " pdb=" N LEU D 160 " pdb=" C LEU D 160 " pdb=" CB LEU D 160 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA GLU D 164 " pdb=" N GLU D 164 " pdb=" C GLU D 164 " pdb=" CB GLU D 164 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA PRO E 197 " pdb=" N PRO E 197 " pdb=" C PRO E 197 " pdb=" CB PRO E 197 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 687 not shown) Planarity restraints: 851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 348 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C LEU E 348 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU E 348 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS E 349 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 240 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO D 241 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 241 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 241 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 88 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO D 89 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 89 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 89 " -0.023 5.00e-02 4.00e+02 ... (remaining 848 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 65 2.57 - 3.15: 4141 3.15 - 3.73: 7324 3.73 - 4.32: 10238 4.32 - 4.90: 16541 Nonbonded interactions: 38309 Sorted by model distance: nonbonded pdb=" OH TYR E 252 " pdb=" OD1 ASP E 341 " model vdw 1.981 3.040 nonbonded pdb=" OH TYR D 252 " pdb=" OD1 ASP D 341 " model vdw 1.998 3.040 nonbonded pdb=" OH TYR D 260 " pdb=" OD2 ASP E 358 " model vdw 2.022 3.040 nonbonded pdb=" O LEU E 160 " pdb=" ND2 ASN E 161 " model vdw 2.061 3.120 nonbonded pdb=" O TYR E 260 " pdb=" OG SER E 261 " model vdw 2.128 3.040 ... (remaining 38304 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 Found NCS groups: ncs_group { reference = (chain 'D' and resid 83 through 365) selection = chain 'E' } 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: 1.410 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.410 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 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 0.032 4764 Z= 0.178 Angle : 0.592 5.193 6433 Z= 0.341 Chirality : 0.040 0.154 690 Planarity : 0.005 0.058 851 Dihedral : 14.698 89.457 1825 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.39 % Allowed : 0.39 % Favored : 99.23 % 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: 0.97 (0.35), residues: 564 helix: 1.50 (0.33), residues: 243 sheet: 0.82 (0.47), residues: 94 loop : -0.31 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 189 HIS 0.003 0.001 HIS D 268 PHE 0.020 0.002 PHE E 188 TYR 0.014 0.002 TYR E 266 ARG 0.006 0.001 ARG E 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 58 average time/residue: 0.2255 time to fit residues: 16.2502 Evaluate side-chains 40 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 160 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 161 ASN ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4764 Z= 0.267 Angle : 0.662 6.097 6433 Z= 0.361 Chirality : 0.045 0.156 690 Planarity : 0.005 0.047 851 Dihedral : 6.190 26.063 606 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.77 % Allowed : 7.34 % Favored : 91.89 % 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: 1.03 (0.35), residues: 564 helix: 1.28 (0.31), residues: 250 sheet: 1.34 (0.45), residues: 92 loop : -0.20 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 189 HIS 0.002 0.001 HIS E 281 PHE 0.028 0.003 PHE E 188 TYR 0.016 0.002 TYR D 84 ARG 0.015 0.001 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 289 MET cc_start: 0.8699 (mmm) cc_final: 0.8489 (mmm) REVERT: D 335 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8319 (mm-30) REVERT: D 346 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7115 (mp0) REVERT: E 349 LYS cc_start: 0.7906 (tttt) cc_final: 0.7676 (tttp) outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 0.2173 time to fit residues: 12.7341 Evaluate side-chains 40 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 352 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 ASN E 268 HIS ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4764 Z= 0.216 Angle : 0.609 6.418 6433 Z= 0.327 Chirality : 0.043 0.153 690 Planarity : 0.005 0.046 851 Dihedral : 6.050 27.321 606 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.35 % Allowed : 8.49 % Favored : 90.15 % 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: 1.03 (0.36), residues: 564 helix: 1.15 (0.31), residues: 262 sheet: 1.19 (0.48), residues: 94 loop : -0.02 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 189 HIS 0.001 0.001 HIS E 281 PHE 0.017 0.002 PHE E 188 TYR 0.023 0.002 TYR D 84 ARG 0.004 0.001 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8445 (mm-30) REVERT: D 346 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7143 (mp0) REVERT: E 346 GLU cc_start: 0.8746 (tp30) cc_final: 0.8466 (tp30) outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 0.2101 time to fit residues: 13.3160 Evaluate side-chains 41 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 274 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.0170 chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4764 Z= 0.181 Angle : 0.586 7.434 6433 Z= 0.311 Chirality : 0.042 0.146 690 Planarity : 0.004 0.039 851 Dihedral : 5.814 26.994 606 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.93 % Allowed : 8.88 % Favored : 89.19 % 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: 1.36 (0.36), residues: 564 helix: 1.46 (0.32), residues: 251 sheet: 1.60 (0.48), residues: 90 loop : 0.05 (0.47), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 359 HIS 0.001 0.000 HIS E 281 PHE 0.016 0.002 PHE D 124 TYR 0.014 0.001 TYR D 84 ARG 0.003 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8521 (mm-30) REVERT: D 352 LEU cc_start: 0.7758 (tp) cc_final: 0.7465 (tt) REVERT: E 266 TYR cc_start: 0.8058 (p90) cc_final: 0.7810 (p90) REVERT: E 346 GLU cc_start: 0.8727 (tp30) cc_final: 0.8421 (tp30) outliers start: 10 outliers final: 7 residues processed: 51 average time/residue: 0.2052 time to fit residues: 13.5312 Evaluate side-chains 46 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4764 Z= 0.202 Angle : 0.585 8.357 6433 Z= 0.308 Chirality : 0.042 0.151 690 Planarity : 0.004 0.038 851 Dihedral : 5.704 26.514 606 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.54 % Allowed : 11.00 % Favored : 87.45 % 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: 1.37 (0.36), residues: 564 helix: 1.49 (0.32), residues: 251 sheet: 1.21 (0.51), residues: 98 loop : 0.18 (0.48), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 189 HIS 0.002 0.001 HIS E 268 PHE 0.014 0.002 PHE D 233 TYR 0.012 0.001 TYR D 84 ARG 0.003 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 212 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: D 335 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8597 (mm-30) REVERT: E 249 CYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8629 (p) REVERT: E 266 TYR cc_start: 0.8113 (p90) cc_final: 0.7876 (p90) REVERT: E 346 GLU cc_start: 0.8715 (tp30) cc_final: 0.8418 (tp30) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 0.2044 time to fit residues: 12.6113 Evaluate side-chains 45 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 249 CYS Chi-restraints excluded: chain E residue 274 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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-5532/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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-5532/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-5532/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-5532/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-5532/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-5532/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-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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-5532/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-5532/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-5532/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-5532/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: 56.8501 > 50: distance: 4 - 29: 17.828 distance: 8 - 35: 25.020 distance: 24 - 29: 20.589 distance: 29 - 30: 25.078 distance: 30 - 31: 32.116 distance: 30 - 33: 21.074 distance: 31 - 32: 17.013 distance: 31 - 35: 48.113 distance: 33 - 34: 21.809 distance: 35 - 36: 23.582 distance: 36 - 37: 36.530 distance: 37 - 38: 9.229 distance: 37 - 39: 20.541 distance: 39 - 40: 10.978 distance: 40 - 41: 26.185 distance: 40 - 43: 27.149 distance: 41 - 42: 16.855 distance: 41 - 48: 22.725 distance: 43 - 44: 18.976 distance: 44 - 45: 21.478 distance: 45 - 46: 18.750 distance: 45 - 47: 12.771 distance: 48 - 49: 21.357 distance: 49 - 50: 20.904 distance: 49 - 52: 33.871 distance: 50 - 51: 38.519 distance: 50 - 57: 11.511 distance: 52 - 53: 15.387 distance: 53 - 54: 6.551 distance: 54 - 55: 13.597 distance: 54 - 56: 12.240 distance: 57 - 58: 17.084 distance: 58 - 59: 24.426 distance: 58 - 61: 49.110 distance: 59 - 60: 31.870 distance: 59 - 66: 15.350 distance: 61 - 62: 19.367 distance: 62 - 63: 26.002 distance: 63 - 64: 19.031 distance: 63 - 65: 24.235 distance: 66 - 67: 8.941 distance: 66 - 72: 20.512 distance: 67 - 68: 20.514 distance: 67 - 70: 23.821 distance: 68 - 69: 17.236 distance: 68 - 73: 18.487 distance: 70 - 71: 10.341 distance: 71 - 72: 16.841 distance: 73 - 74: 9.948 distance: 74 - 75: 16.748 distance: 74 - 77: 13.987 distance: 75 - 76: 32.331 distance: 75 - 82: 12.241 distance: 76 - 107: 30.704 distance: 78 - 79: 17.060 distance: 79 - 80: 16.601 distance: 80 - 81: 10.866 distance: 82 - 83: 11.512 distance: 82 - 88: 26.201 distance: 83 - 84: 26.372 distance: 83 - 86: 16.617 distance: 84 - 85: 4.162 distance: 84 - 89: 14.922 distance: 85 - 115: 9.440 distance: 86 - 87: 11.155 distance: 87 - 88: 19.267 distance: 89 - 90: 20.921 distance: 90 - 91: 10.599 distance: 90 - 93: 22.064 distance: 91 - 92: 15.114 distance: 91 - 98: 9.193 distance: 92 - 120: 19.383 distance: 93 - 94: 17.537 distance: 94 - 95: 9.406 distance: 95 - 96: 7.514 distance: 95 - 97: 4.330 distance: 98 - 99: 7.364 distance: 99 - 100: 20.564 distance: 99 - 102: 20.813 distance: 100 - 101: 5.936 distance: 100 - 107: 21.304 distance: 101 - 126: 26.876 distance: 102 - 103: 17.371 distance: 103 - 104: 12.015 distance: 104 - 105: 6.308 distance: 104 - 106: 8.176