Starting phenix.real_space_refine on Fri Aug 22 16:50:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vq4_32085/08_2025/7vq4_32085.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vq4_32085/08_2025/7vq4_32085.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 { model { file = "/net/cci-nas-00/data/ceres_data/7vq4_32085/08_2025/7vq4_32085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vq4_32085/08_2025/7vq4_32085.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vq4_32085/08_2025/7vq4_32085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vq4_32085/08_2025/7vq4_32085.map" } resolution = 3.2 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= 0.005 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 34 5.16 5 C 4070 2.51 5 N 1052 2.21 5 O 1150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s 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: 6306 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Time building chain proxies: 1.75, per 1000 atoms: 0.28 Number of scatterers: 6306 At special positions: 0 Unit cell: (82.134, 84.162, 111.54, 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 34 16.00 O 1150 8.00 N 1052 7.00 C 4070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 393.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 84.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 removed outlier: 3.624A pdb=" N ASP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.863A pdb=" N GLY A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 Processing helix chain 'A' and resid 69 through 102 removed outlier: 3.756A pdb=" N THR A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 125 Processing helix chain 'A' and resid 127 through 134 removed outlier: 3.524A pdb=" N LYS A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 151 removed outlier: 3.601A pdb=" N SER A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 183 Processing helix chain 'A' and resid 187 through 214 removed outlier: 3.694A pdb=" N ASP A 191 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 241 removed outlier: 4.615A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 267 through 293 removed outlier: 3.720A pdb=" N TYR A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 306 removed outlier: 3.833A pdb=" N LYS A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 330 removed outlier: 3.738A pdb=" N LEU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 removed outlier: 4.368A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 398 Processing helix chain 'B' and resid 2 through 18 removed outlier: 3.624A pdb=" N ASP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 41 removed outlier: 3.864A pdb=" N GLY B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 Processing helix chain 'B' and resid 69 through 102 removed outlier: 3.757A pdb=" N THR B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 125 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.523A pdb=" N LYS B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.601A pdb=" N SER B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 183 Processing helix chain 'B' and resid 187 through 214 removed outlier: 3.693A pdb=" N ASP B 191 " --> pdb=" O TRP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 removed outlier: 4.615A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 Processing helix chain 'B' and resid 267 through 293 removed outlier: 3.720A pdb=" N TYR B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 306 removed outlier: 3.833A pdb=" N LYS B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 330 removed outlier: 3.737A pdb=" N LEU B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 330 " --> pdb=" O ILE B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 removed outlier: 4.368A pdb=" N ILE B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 398 509 hydrogen bonds defined for protein. 1527 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: 0.97 Time building geometry restraints manager: 0.80 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: 2008 1.34 - 1.46: 1045 1.46 - 1.57: 3321 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6434 Sorted by residual: bond pdb=" CB TRP B 57 " pdb=" CG TRP B 57 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.05e+00 bond pdb=" CB TRP A 57 " pdb=" CG TRP A 57 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.04e+00 bond pdb=" CB TRP B 187 " pdb=" CG TRP B 187 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.63e+00 bond pdb=" CB TRP A 187 " pdb=" CG TRP A 187 " ideal model delta sigma weight residual 1.498 1.459 0.039 3.10e-02 1.04e+03 1.62e+00 bond pdb=" CA VAL A 186 " pdb=" C VAL A 186 " ideal model delta sigma weight residual 1.527 1.518 0.009 8.50e-03 1.38e+04 1.14e+00 ... (remaining 6429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 8313 1.50 - 3.01: 299 3.01 - 4.51: 56 4.51 - 6.01: 20 6.01 - 7.52: 4 Bond angle restraints: 8692 Sorted by residual: angle pdb=" N VAL B 105 " pdb=" CA VAL B 105 " pdb=" C VAL B 105 " ideal model delta sigma weight residual 112.17 108.66 3.51 9.50e-01 1.11e+00 1.36e+01 angle pdb=" N VAL A 105 " pdb=" CA VAL A 105 " pdb=" C VAL A 105 " ideal model delta sigma weight residual 112.17 108.67 3.50 9.50e-01 1.11e+00 1.36e+01 angle pdb=" N PHE B 134 " pdb=" CA PHE B 134 " pdb=" C PHE B 134 " ideal model delta sigma weight residual 110.44 114.21 -3.77 1.20e+00 6.94e-01 9.89e+00 angle pdb=" N PHE A 134 " pdb=" CA PHE A 134 " pdb=" C PHE A 134 " ideal model delta sigma weight residual 110.44 114.16 -3.72 1.20e+00 6.94e-01 9.62e+00 angle pdb=" CA PRO B 267 " pdb=" C PRO B 267 " pdb=" O PRO B 267 " ideal model delta sigma weight residual 123.07 119.36 3.71 1.38e+00 5.25e-01 7.22e+00 ... (remaining 8687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 3396 18.03 - 36.05: 366 36.05 - 54.08: 62 54.08 - 72.10: 26 72.10 - 90.13: 6 Dihedral angle restraints: 3856 sinusoidal: 1532 harmonic: 2324 Sorted by residual: dihedral pdb=" CA CYS A 184 " pdb=" C CYS A 184 " pdb=" N PRO A 185 " pdb=" CA PRO A 185 " ideal model delta harmonic sigma weight residual -180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA CYS B 184 " pdb=" C CYS B 184 " pdb=" N PRO B 185 " pdb=" CA PRO B 185 " ideal model delta harmonic sigma weight residual -180.00 -159.70 -20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA HIS B 259 " pdb=" C HIS B 259 " pdb=" N GLY B 260 " pdb=" CA GLY B 260 " ideal model delta harmonic sigma weight residual -180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 499 0.030 - 0.060: 357 0.060 - 0.090: 105 0.090 - 0.119: 30 0.119 - 0.149: 5 Chirality restraints: 996 Sorted by residual: chirality pdb=" CA PRO B 365 " pdb=" N PRO B 365 " pdb=" C PRO B 365 " pdb=" CB PRO B 365 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA PRO A 365 " pdb=" N PRO A 365 " pdb=" C PRO A 365 " pdb=" CB PRO A 365 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 332 " pdb=" N ILE A 332 " pdb=" C ILE A 332 " pdb=" CB ILE A 332 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 993 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 364 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A 365 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 364 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO B 365 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 365 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 365 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 127 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 128 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 128 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 128 " 0.021 5.00e-02 4.00e+02 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 239 2.70 - 3.25: 6944 3.25 - 3.80: 10031 3.80 - 4.35: 11847 4.35 - 4.90: 20167 Nonbonded interactions: 49228 Sorted by model distance: nonbonded pdb=" OD1 ASP A 295 " pdb=" N PHE A 296 " model vdw 2.155 3.120 nonbonded pdb=" OD1 ASP B 295 " pdb=" N PHE B 296 " model vdw 2.155 3.120 nonbonded pdb=" O MET B 1 " pdb=" N ARG B 5 " model vdw 2.178 3.120 nonbonded pdb=" OH TYR A 291 " pdb=" OG SER B 376 " model vdw 2.209 3.040 nonbonded pdb=" NH1 ARG A 80 " pdb=" OH TYR A 136 " model vdw 2.225 3.120 ... (remaining 49223 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.330 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.700 Find NCS groups from input model: 0.040 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.007 0.044 6434 Z= 0.317 Angle : 0.740 7.518 8692 Z= 0.423 Chirality : 0.042 0.149 996 Planarity : 0.004 0.050 1090 Dihedral : 16.105 90.127 2352 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.30 % Allowed : 8.62 % Favored : 89.08 % 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: -1.96 (0.27), residues: 792 helix: -0.72 (0.18), residues: 666 sheet: None (None), residues: 0 loop : -3.76 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 13 TYR 0.013 0.002 TYR B 291 PHE 0.018 0.002 PHE B 153 TRP 0.007 0.001 TRP B 255 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00685 ( 6434) covalent geometry : angle 0.73974 ( 8692) hydrogen bonds : bond 0.12719 ( 509) hydrogen bonds : angle 5.74557 ( 1527) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.265 Fit side-chains REVERT: A 40 TYR cc_start: 0.8043 (t80) cc_final: 0.7503 (t80) REVERT: A 180 SER cc_start: 0.9003 (t) cc_final: 0.8580 (p) REVERT: A 237 LYS cc_start: 0.8450 (mttt) cc_final: 0.8150 (mtmt) REVERT: A 306 LEU cc_start: 0.8688 (tp) cc_final: 0.8481 (tp) REVERT: A 307 GLU cc_start: 0.7515 (pt0) cc_final: 0.7258 (pm20) REVERT: A 322 LYS cc_start: 0.7820 (tptm) cc_final: 0.7412 (ttpt) REVERT: B 1 MET cc_start: 0.5033 (OUTLIER) cc_final: 0.4477 (ptp) REVERT: B 40 TYR cc_start: 0.8064 (t80) cc_final: 0.7540 (t80) REVERT: B 328 LEU cc_start: 0.9183 (tp) cc_final: 0.8902 (tp) outliers start: 16 outliers final: 7 residues processed: 216 average time/residue: 0.0967 time to fit residues: 26.1155 Evaluate side-chains 162 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 223 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS A 54 ASN A 251 ASN A 259 HIS A 293 ASN A 340 HIS A 343 ASN B 24 HIS B 54 ASN B 259 HIS B 280 GLN B 293 ASN B 330 GLN B 340 HIS B 343 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.158761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.130194 restraints weight = 9378.621| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.63 r_work: 0.3605 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6434 Z= 0.142 Angle : 0.556 5.780 8692 Z= 0.293 Chirality : 0.038 0.146 996 Planarity : 0.004 0.046 1090 Dihedral : 5.485 50.362 870 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.74 % Allowed : 15.66 % Favored : 79.60 % 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: 1.25 (0.30), residues: 792 helix: 1.59 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -3.18 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 265 TYR 0.013 0.001 TYR B 236 PHE 0.013 0.001 PHE A 145 TRP 0.009 0.001 TRP A 57 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6434) covalent geometry : angle 0.55602 ( 8692) hydrogen bonds : bond 0.05174 ( 509) hydrogen bonds : angle 3.92526 ( 1527) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8405 (pp30) REVERT: A 105 VAL cc_start: 0.6426 (OUTLIER) cc_final: 0.6055 (t) REVERT: A 159 MET cc_start: 0.7039 (ptt) cc_final: 0.6610 (mtm) REVERT: A 180 SER cc_start: 0.8999 (t) cc_final: 0.8438 (p) REVERT: A 193 HIS cc_start: 0.7857 (OUTLIER) cc_final: 0.7056 (t-90) REVERT: A 201 ASP cc_start: 0.8322 (t0) cc_final: 0.8052 (t0) REVERT: A 237 LYS cc_start: 0.8369 (mttt) cc_final: 0.7996 (mtmt) REVERT: A 263 ARG cc_start: 0.8039 (tpp80) cc_final: 0.7180 (tmt170) REVERT: A 286 ASP cc_start: 0.8632 (t70) cc_final: 0.8362 (t0) REVERT: A 321 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7597 (mmt) REVERT: A 322 LYS cc_start: 0.7649 (tptm) cc_final: 0.6999 (ttpt) REVERT: A 368 MET cc_start: 0.8116 (mmm) cc_final: 0.7906 (mmm) REVERT: B 1 MET cc_start: 0.4605 (ttt) cc_final: 0.4179 (tpp) REVERT: B 9 ARG cc_start: 0.6167 (mtt-85) cc_final: 0.5416 (ptp90) REVERT: B 154 ARG cc_start: 0.7495 (mtp-110) cc_final: 0.7245 (mtm110) REVERT: B 193 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.7206 (t-90) REVERT: B 201 ASP cc_start: 0.8298 (t0) cc_final: 0.8010 (t0) REVERT: B 328 LEU cc_start: 0.9038 (tp) cc_final: 0.8614 (tp) REVERT: B 377 MET cc_start: 0.8621 (mmt) cc_final: 0.8276 (mmm) outliers start: 33 outliers final: 20 residues processed: 190 average time/residue: 0.0766 time to fit residues: 18.9891 Evaluate side-chains 177 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 50.0618 > 50: distance: 2 - 29: 8.996 distance: 6 - 41: 17.045 distance: 21 - 29: 9.342 distance: 29 - 30: 3.521 distance: 30 - 31: 6.034 distance: 30 - 33: 10.502 distance: 31 - 32: 9.732 distance: 31 - 41: 7.650 distance: 33 - 34: 3.674 distance: 34 - 36: 5.159 distance: 35 - 37: 7.899 distance: 36 - 38: 3.787 distance: 37 - 39: 4.881 distance: 38 - 39: 3.838 distance: 39 - 40: 3.838 distance: 41 - 42: 14.192 distance: 42 - 43: 7.503 distance: 42 - 45: 14.244 distance: 43 - 44: 24.786 distance: 43 - 53: 6.753 distance: 45 - 46: 5.263 distance: 47 - 49: 4.407 distance: 50 - 51: 3.959 distance: 51 - 52: 3.494 distance: 53 - 54: 11.456 distance: 54 - 55: 14.800 distance: 54 - 57: 15.514 distance: 55 - 56: 9.882 distance: 55 - 62: 21.842 distance: 57 - 58: 5.412 distance: 58 - 59: 25.819 distance: 59 - 60: 17.794 distance: 59 - 61: 16.031 distance: 62 - 63: 9.972 distance: 62 - 68: 13.597 distance: 63 - 64: 23.890 distance: 63 - 66: 13.771 distance: 64 - 65: 15.198 distance: 64 - 69: 11.094 distance: 66 - 67: 19.415 distance: 67 - 68: 3.946 distance: 69 - 70: 8.878 distance: 70 - 71: 7.776 distance: 70 - 73: 14.067 distance: 71 - 72: 20.915 distance: 71 - 80: 15.034 distance: 73 - 74: 12.966 distance: 74 - 75: 9.048 distance: 74 - 76: 5.132 distance: 75 - 77: 10.206 distance: 76 - 78: 3.752 distance: 77 - 79: 4.683 distance: 78 - 79: 9.093 distance: 80 - 81: 12.382 distance: 82 - 83: 17.060 distance: 84 - 85: 4.223 distance: 84 - 90: 11.617 distance: 85 - 86: 5.595 distance: 85 - 88: 17.413 distance: 86 - 87: 14.783 distance: 86 - 91: 17.155 distance: 88 - 89: 3.743 distance: 89 - 90: 13.682 distance: 91 - 92: 13.944 distance: 92 - 93: 5.860 distance: 92 - 95: 6.068 distance: 93 - 94: 32.032 distance: 93 - 102: 12.961 distance: 95 - 96: 14.049 distance: 96 - 97: 11.473 distance: 96 - 98: 9.221 distance: 97 - 99: 8.072 distance: 98 - 100: 11.392 distance: 99 - 101: 6.973 distance: 100 - 101: 9.157 distance: 102 - 103: 15.210 distance: 103 - 104: 9.998 distance: 103 - 106: 8.421 distance: 104 - 105: 28.760 distance: 104 - 109: 10.912 distance: 106 - 107: 22.418 distance: 106 - 108: 16.624 distance: 109 - 110: 8.524 distance: 110 - 111: 9.605 distance: 110 - 113: 12.074 distance: 111 - 112: 13.706 distance: 111 - 117: 11.101 distance: 113 - 114: 15.948 distance: 114 - 115: 16.522 distance: 114 - 116: 20.168