Starting phenix.real_space_refine on Fri Aug 22 12:56:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vv6_32139/08_2025/7vv6_32139.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vv6_32139/08_2025/7vv6_32139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vv6_32139/08_2025/7vv6_32139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vv6_32139/08_2025/7vv6_32139.map" model { file = "/net/cci-nas-00/data/ceres_data/7vv6_32139/08_2025/7vv6_32139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vv6_32139/08_2025/7vv6_32139.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 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 18 5.16 5 C 1518 2.51 5 N 342 2.21 5 O 349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2227 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2161 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'6IB': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.67, per 1000 atoms: 0.30 Number of scatterers: 2227 At special positions: 0 Unit cell: (65.224, 72.588, 61.016, 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 18 16.00 O 349 8.00 N 342 7.00 C 1518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 258 " distance=2.04 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.15 Conformation dependent library (CDL) restraints added in 52.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 508 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 84.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'R' and resid 30 through 57 removed outlier: 3.529A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 94 removed outlier: 3.831A pdb=" N VAL R 66 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 3.602A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 168 Processing helix chain 'R' and resid 176 through 212 removed outlier: 3.926A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 236 Processing helix chain 'R' and resid 236 through 245 removed outlier: 4.339A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 256 through 280 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 280 through 285 Processing helix chain 'R' and resid 286 through 288 No H-bonds generated for 'chain 'R' and resid 286 through 288' 169 hydrogen bonds defined for protein. 507 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.21 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 617 1.34 - 1.47: 662 1.47 - 1.59: 993 1.59 - 1.71: 1 1.71 - 1.84: 22 Bond restraints: 2295 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.669 -0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.335 1.368 -0.034 1.28e-02 6.10e+03 6.99e+00 bond pdb=" C31 6IB R 402 " pdb=" N5 6IB R 402 " ideal model delta sigma weight residual 1.447 1.496 -0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" C32 6IB R 402 " pdb=" N6 6IB R 402 " ideal model delta sigma weight residual 1.449 1.497 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" CB VAL R 131 " pdb=" CG2 VAL R 131 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.00e+00 ... (remaining 2290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 3010 3.21 - 6.43: 103 6.43 - 9.64: 14 9.64 - 12.86: 2 12.86 - 16.07: 2 Bond angle restraints: 3131 Sorted by residual: angle pdb=" N LEU R 237 " pdb=" CA LEU R 237 " pdb=" C LEU R 237 " ideal model delta sigma weight residual 113.45 120.88 -7.43 1.39e+00 5.18e-01 2.85e+01 angle pdb=" C TRP R 250 " pdb=" N LYS R 251 " pdb=" CA LYS R 251 " ideal model delta sigma weight residual 122.08 129.29 -7.21 1.47e+00 4.63e-01 2.41e+01 angle pdb=" C GLY R 236 " pdb=" N LEU R 237 " pdb=" CA LEU R 237 " ideal model delta sigma weight residual 120.58 127.01 -6.43 1.32e+00 5.74e-01 2.37e+01 angle pdb=" CA LEU R 226 " pdb=" CB LEU R 226 " pdb=" CG LEU R 226 " ideal model delta sigma weight residual 116.30 132.37 -16.07 3.50e+00 8.16e-02 2.11e+01 angle pdb=" N SER R 177 " pdb=" CA SER R 177 " pdb=" C SER R 177 " ideal model delta sigma weight residual 111.28 115.95 -4.67 1.09e+00 8.42e-01 1.83e+01 ... (remaining 3126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.72: 1034 12.72 - 25.44: 169 25.44 - 38.16: 97 38.16 - 50.88: 34 50.88 - 63.60: 21 Dihedral angle restraints: 1355 sinusoidal: 571 harmonic: 784 Sorted by residual: dihedral pdb=" CA THR R 30 " pdb=" C THR R 30 " pdb=" N LEU R 31 " pdb=" CA LEU R 31 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP R 254 " pdb=" C ASP R 254 " pdb=" N VAL R 255 " pdb=" CA VAL R 255 " ideal model delta harmonic sigma weight residual 180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ASP R 252 " pdb=" C ASP R 252 " pdb=" N SER R 253 " pdb=" CA SER R 253 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 1352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 253 0.061 - 0.122: 88 0.122 - 0.183: 23 0.183 - 0.244: 2 0.244 - 0.305: 2 Chirality restraints: 368 Sorted by residual: chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C9 CLR R 401 " pdb=" C10 CLR R 401 " pdb=" C11 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.70 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA LEU R 237 " pdb=" N LEU R 237 " pdb=" C LEU R 237 " pdb=" CB LEU R 237 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 365 not shown) Planarity restraints: 361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 149 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C VAL R 149 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL R 149 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS R 150 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 43 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C VAL R 43 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL R 43 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY R 44 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 40 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C ILE R 40 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE R 40 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA R 41 " -0.013 2.00e-02 2.50e+03 ... (remaining 358 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 629 2.81 - 3.33: 1941 3.33 - 3.86: 3854 3.86 - 4.38: 4171 4.38 - 4.90: 7427 Nonbonded interactions: 18022 Sorted by model distance: nonbonded pdb=" O GLY R 27 " pdb=" OH TYR R 89 " model vdw 2.291 3.040 nonbonded pdb=" O SER R 264 " pdb=" OG SER R 268 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.320 3.040 nonbonded pdb=" O SER R 98 " pdb=" OG SER R 98 " model vdw 2.322 3.040 nonbonded pdb=" O THR R 107 " pdb=" OG SER R 161 " model vdw 2.322 3.040 ... (remaining 18017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.060 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 : 0.010 0.134 2297 Z= 0.435 Angle : 1.380 16.073 3135 Z= 0.708 Chirality : 0.068 0.305 368 Planarity : 0.009 0.048 361 Dihedral : 19.052 63.599 841 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 10.37 % Allowed : 24.90 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.22 (0.34), residues: 269 helix: -2.49 (0.23), residues: 208 sheet: None (None), residues: 0 loop : -3.08 (0.63), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 138 TYR 0.021 0.004 TYR R 89 PHE 0.020 0.003 PHE R 183 TRP 0.015 0.003 TRP R 289 HIS 0.004 0.001 HIS R 261 Details of bonding type rmsd covalent geometry : bond 0.00979 ( 2295) covalent geometry : angle 1.37952 ( 3131) SS BOND : bond 0.00539 ( 2) SS BOND : angle 1.88847 ( 4) hydrogen bonds : bond 0.11723 ( 169) hydrogen bonds : angle 6.91330 ( 507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.052 Fit side-chains revert: symmetry clash REVERT: R 109 MET cc_start: 0.8310 (ttp) cc_final: 0.7998 (ttm) REVERT: R 164 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7868 (tm-30) REVERT: R 166 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8433 (tptt) REVERT: R 201 SER cc_start: 0.9194 (m) cc_final: 0.8684 (p) REVERT: R 242 GLN cc_start: 0.8817 (pp30) cc_final: 0.8517 (pp30) outliers start: 25 outliers final: 1 residues processed: 67 average time/residue: 0.0316 time to fit residues: 2.6051 Evaluate side-chains 31 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 182 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.0050 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 HIS R 271 ASN R 275 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.082137 restraints weight = 3711.859| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.35 r_work: 0.2832 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2297 Z= 0.129 Angle : 0.638 9.140 3135 Z= 0.308 Chirality : 0.042 0.208 368 Planarity : 0.005 0.033 361 Dihedral : 10.680 57.262 380 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.90 % Allowed : 27.39 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.49), residues: 269 helix: 0.54 (0.33), residues: 219 sheet: None (None), residues: 0 loop : -2.09 (0.80), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 143 TYR 0.012 0.002 TYR R 222 PHE 0.011 0.001 PHE R 81 TRP 0.012 0.001 TRP R 248 HIS 0.001 0.001 HIS R 144 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 2295) covalent geometry : angle 0.63791 ( 3131) SS BOND : bond 0.00187 ( 2) SS BOND : angle 0.76867 ( 4) hydrogen bonds : bond 0.04208 ( 169) hydrogen bonds : angle 4.40344 ( 507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.051 Fit side-chains revert: symmetry clash REVERT: R 109 MET cc_start: 0.8890 (ttp) cc_final: 0.8611 (ttm) REVERT: R 126 GLU cc_start: 0.9021 (tp30) cc_final: 0.8645 (mm-30) REVERT: R 143 ARG cc_start: 0.8409 (ptm-80) cc_final: 0.8190 (ptm-80) REVERT: R 164 GLU cc_start: 0.8235 (tm-30) cc_final: 0.8025 (tm-30) REVERT: R 166 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8254 (tptt) outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.0416 time to fit residues: 2.0823 Evaluate side-chains 34 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 182 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.104676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.079385 restraints weight = 4006.575| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.31 r_work: 0.2790 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2297 Z= 0.150 Angle : 0.589 6.408 3135 Z= 0.288 Chirality : 0.042 0.156 368 Planarity : 0.004 0.031 361 Dihedral : 9.465 60.682 380 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.49 % Allowed : 27.39 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.52), residues: 269 helix: 1.65 (0.35), residues: 219 sheet: None (None), residues: 0 loop : -1.73 (0.86), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 143 TYR 0.013 0.002 TYR R 222 PHE 0.010 0.001 PHE R 244 TRP 0.008 0.001 TRP R 243 HIS 0.002 0.001 HIS R 144 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 2295) covalent geometry : angle 0.58896 ( 3131) SS BOND : bond 0.00043 ( 2) SS BOND : angle 0.58335 ( 4) hydrogen bonds : bond 0.04278 ( 169) hydrogen bonds : angle 4.06461 ( 507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.087 Fit side-chains REVERT: R 109 MET cc_start: 0.8863 (ttp) cc_final: 0.8597 (ttm) REVERT: R 166 LYS cc_start: 0.9038 (ttpp) cc_final: 0.8419 (tptt) REVERT: R 176 ASP cc_start: 0.7314 (p0) cc_final: 0.7050 (p0) REVERT: R 201 SER cc_start: 0.9365 (m) cc_final: 0.8939 (p) REVERT: R 242 GLN cc_start: 0.9187 (pp30) cc_final: 0.8947 (pp30) outliers start: 6 outliers final: 5 residues processed: 36 average time/residue: 0.0628 time to fit residues: 2.6757 Evaluate side-chains 33 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.7931 > 50: distance: 25 - 45: 3.374 distance: 29 - 53: 14.331 distance: 34 - 61: 28.202 distance: 38 - 41: 3.071 distance: 40 - 67: 9.537 distance: 42 - 43: 5.693 distance: 42 - 44: 6.760 distance: 45 - 46: 3.224 distance: 46 - 47: 4.442 distance: 46 - 49: 4.267 distance: 47 - 48: 6.212 distance: 47 - 53: 6.438 distance: 48 - 75: 8.054 distance: 50 - 51: 4.716 distance: 50 - 52: 3.972 distance: 54 - 55: 6.818 distance: 54 - 57: 6.460 distance: 55 - 56: 10.787 distance: 55 - 61: 21.548 distance: 56 - 83: 7.199 distance: 57 - 58: 6.239 distance: 58 - 59: 4.267 distance: 58 - 60: 13.509 distance: 61 - 62: 31.781 distance: 62 - 63: 8.533 distance: 62 - 65: 27.277 distance: 63 - 64: 6.471 distance: 63 - 67: 9.636 distance: 64 - 92: 10.918 distance: 65 - 66: 10.384 distance: 67 - 68: 5.383 distance: 68 - 69: 3.664 distance: 68 - 71: 3.639 distance: 69 - 70: 3.018 distance: 69 - 75: 3.477 distance: 70 - 96: 5.265 distance: 71 - 72: 4.870 distance: 72 - 74: 3.962 distance: 76 - 79: 4.787 distance: 77 - 78: 3.041 distance: 78 - 105: 4.607 distance: 79 - 80: 3.432 distance: 80 - 81: 5.755 distance: 80 - 82: 3.246 distance: 84 - 85: 3.410 distance: 84 - 87: 4.624 distance: 85 - 92: 5.336 distance: 86 - 116: 9.160 distance: 87 - 88: 3.835 distance: 89 - 90: 4.170 distance: 89 - 91: 7.601 distance: 93 - 94: 5.718 distance: 94 - 95: 4.011 distance: 94 - 96: 5.378 distance: 97 - 98: 3.460 distance: 97 - 100: 3.397 distance: 98 - 99: 7.967 distance: 98 - 105: 5.268 distance: 100 - 101: 5.863 distance: 101 - 102: 9.525 distance: 102 - 103: 8.258 distance: 103 - 104: 15.641 distance: 107 - 108: 7.640 distance: 109 - 110: 5.370 distance: 110 - 111: 9.208 distance: 110 - 112: 9.631 distance: 111 - 113: 4.778 distance: 113 - 115: 8.201 distance: 114 - 115: 8.518 distance: 148 - 159: 3.354 distance: 163 - 175: 3.337