Starting phenix.real_space_refine on Wed Jul 1 23:57:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrv_37791/07_2026/8wrv_37791.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrv_37791/07_2026/8wrv_37791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrv_37791/07_2026/8wrv_37791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrv_37791/07_2026/8wrv_37791.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrv_37791/07_2026/8wrv_37791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrv_37791/07_2026/8wrv_37791.cif" } resolution = 3.28 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 92 5.49 5 S 11 5.16 5 C 2479 2.51 5 N 813 2.21 5 O 1076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4471 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 580 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2537 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 3 Chain: "B" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1188 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 23, 'rna3p_pyr': 27} Link IDs: {'rna2p': 6, 'rna3p': 49} Time building chain proxies: 1.13, per 1000 atoms: 0.25 Number of scatterers: 4471 At special positions: 0 Unit cell: (60.72, 77.22, 114.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 P 92 15.00 O 1076 8.00 N 813 7.00 C 2479 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: 0.40 Conformation dependent library (CDL) restraints added in 95.0 milliseconds 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 598 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 4 sheets defined 37.3% alpha, 20.9% beta 24 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 15 through 41 removed outlier: 3.756A pdb=" N HIS A 26 " --> pdb=" O TYR A 22 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.506A pdb=" N THR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 removed outlier: 4.118A pdb=" N SER A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.534A pdb=" N LEU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.597A pdb=" N LEU A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 199 removed outlier: 3.552A pdb=" N LEU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 237 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 3.998A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 6 removed outlier: 5.852A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG A 428 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR A 434 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A 426 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE A 436 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE A 424 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ASP A 438 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS A 422 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 417 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 407 " --> pdb=" O TYR A 417 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 394 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR A 408 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN A 392 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 360 through 363 removed outlier: 3.817A pdb=" N PHE A 369 " --> pdb=" O ALA A 384 " (cutoff:3.500A) 106 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 0.71 Time building geometry restraints manager: 0.52 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: 1019 1.33 - 1.45: 1438 1.45 - 1.57: 2091 1.57 - 1.69: 181 1.69 - 1.81: 16 Bond restraints: 4745 Sorted by residual: bond pdb=" O3' A B -10 " pdb=" P G B -9 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.50e-02 4.44e+03 1.31e+01 bond pdb=" C3' DT C -12 " pdb=" C2' DT C -12 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" N9 G B -4 " pdb=" C4 G B -4 " ideal model delta sigma weight residual 1.375 1.400 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C1' DC C -9 " pdb=" N1 DC C -9 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.66e+00 bond pdb=" C SER A 345 " pdb=" N PRO A 346 " ideal model delta sigma weight residual 1.331 1.368 -0.037 1.31e-02 5.83e+03 8.06e+00 ... (remaining 4740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 6585 2.05 - 4.11: 218 4.11 - 6.16: 20 6.16 - 8.21: 2 8.21 - 10.27: 1 Bond angle restraints: 6826 Sorted by residual: angle pdb=" N3 DT C 5 " pdb=" C4 DT C 5 " pdb=" O4 DT C 5 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" C1' G B -4 " pdb=" N9 G B -4 " pdb=" C4 G B -4 " ideal model delta sigma weight residual 126.50 131.91 -5.41 1.30e+00 5.92e-01 1.73e+01 angle pdb=" N3 DT D 7 " pdb=" C4 DT D 7 " pdb=" O4 DT D 7 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT C 3 " pdb=" C4 DT C 3 " pdb=" O4 DT C 3 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT D 5 " pdb=" C4 DT D 5 " pdb=" O4 DT D 5 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 ... (remaining 6821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 2533 35.81 - 71.62: 278 71.62 - 107.43: 26 107.43 - 143.24: 2 143.24 - 179.05: 3 Dihedral angle restraints: 2842 sinusoidal: 1921 harmonic: 921 Sorted by residual: dihedral pdb=" O4' C B -6 " pdb=" C1' C B -6 " pdb=" N1 C B -6 " pdb=" C2 C B -6 " ideal model delta sinusoidal sigma weight residual 200.00 50.44 149.56 1 1.50e+01 4.44e-03 7.95e+01 dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual 200.00 53.31 146.69 1 1.50e+01 4.44e-03 7.83e+01 dihedral pdb=" O4' U B -5 " pdb=" C1' U B -5 " pdb=" N1 U B -5 " pdb=" C2 U B -5 " ideal model delta sinusoidal sigma weight residual -128.00 51.05 -179.05 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 2839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 687 0.070 - 0.141: 88 0.141 - 0.211: 22 0.211 - 0.282: 1 0.282 - 0.352: 2 Chirality restraints: 800 Sorted by residual: chirality pdb=" CA ARG A 41 " pdb=" N ARG A 41 " pdb=" C ARG A 41 " pdb=" CB ARG A 41 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA ARG A 172 " pdb=" N ARG A 172 " pdb=" C ARG A 172 " pdb=" CB ARG A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2' G B -36 " pdb=" C3' G B -36 " pdb=" O2' G B -36 " pdb=" C1' G B -36 " both_signs ideal model delta sigma weight residual False -2.75 -2.53 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 797 not shown) Planarity restraints: 547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 92 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A 93 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 205 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.26e+00 pdb=" C SER A 205 " -0.031 2.00e-02 2.50e+03 pdb=" O SER A 205 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 206 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 202 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO A 203 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " -0.023 5.00e-02 4.00e+02 ... (remaining 544 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1207 2.82 - 3.34: 3916 3.34 - 3.86: 8362 3.86 - 4.38: 9413 4.38 - 4.90: 13668 Nonbonded interactions: 36566 Sorted by model distance: nonbonded pdb=" NH2 ARG A 47 " pdb=" OE2 GLU A 53 " model vdw 2.301 3.120 nonbonded pdb=" O2' C B -30 " pdb=" OP2 U B -29 " model vdw 2.351 3.040 nonbonded pdb=" O2 U B -27 " pdb=" N2 G B -12 " model vdw 2.358 2.496 nonbonded pdb=" OG1 THR A 338 " pdb=" OP1 A B 5 " model vdw 2.368 3.040 nonbonded pdb=" OP1 DA C 2 " pdb=" NZ LYS A 422 " model vdw 2.397 3.120 ... (remaining 36561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.180 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.080 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 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 : 0.005 0.054 4745 Z= 0.390 Angle : 0.787 10.266 6826 Z= 0.614 Chirality : 0.054 0.352 800 Planarity : 0.005 0.051 547 Dihedral : 23.712 179.047 2244 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.85 % Allowed : 0.74 % Favored : 97.41 % 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 are not related in a simple way. whole: -1.76 (0.47), residues: 308 helix: -0.50 (0.48), residues: 109 sheet: -1.31 (0.54), residues: 77 loop : -1.51 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 12 TYR 0.010 0.001 TYR A 22 PHE 0.021 0.001 PHE A 83 TRP 0.020 0.003 TRP A 229 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.39 ( 4745) covalent geometry : angle 0.78686 / 0.61 ( 6826) hydrogen bonds : bond 0.16282 / 18.46 ( 165) hydrogen bonds : angle 7.07049 / 8.45 ( 412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.136 Fit side-chains REVERT: A 102 GLU cc_start: 0.7126 (pm20) cc_final: 0.6910 (pm20) REVERT: A 437 ILE cc_start: 0.8140 (mm) cc_final: 0.7937 (mm) outliers start: 5 outliers final: 0 residues processed: 62 average time/residue: 0.1403 time to fit residues: 9.9742 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.182354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.145460 restraints weight = 6659.109| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.58 r_work: 0.3672 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4745 Z= 0.228 Angle : 0.656 8.958 6826 Z= 0.385 Chirality : 0.045 0.268 800 Planarity : 0.007 0.056 547 Dihedral : 25.693 179.604 1619 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.37 % Allowed : 9.26 % Favored : 90.37 % 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 are not related in a simple way. whole: -1.32 (0.47), residues: 308 helix: 0.19 (0.47), residues: 112 sheet: -1.13 (0.56), residues: 77 loop : -1.60 (0.59), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 47 TYR 0.012 0.002 TYR A 22 PHE 0.019 0.002 PHE A 369 TRP 0.010 0.002 TRP A 229 HIS 0.007 0.002 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.23 ( 4745) covalent geometry : angle 0.65645 / 0.38 ( 6826) hydrogen bonds : bond 0.05768 / 6.26 ( 165) hydrogen bonds : angle 4.55596 / 5.43 ( 412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.118 Fit side-chains REVERT: A 96 ARG cc_start: 0.8190 (mmt90) cc_final: 0.7937 (mmm-85) REVERT: A 102 GLU cc_start: 0.7625 (pm20) cc_final: 0.7377 (pm20) REVERT: A 190 MET cc_start: 0.7736 (tpp) cc_final: 0.7530 (tpt) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.1218 time to fit residues: 7.3022 Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 27 optimal weight: 0.2980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.183665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.146742 restraints weight = 6591.763| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.56 r_work: 0.3679 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4745 Z= 0.164 Angle : 0.567 7.494 6826 Z= 0.339 Chirality : 0.041 0.244 800 Planarity : 0.005 0.053 547 Dihedral : 25.672 179.107 1619 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.37 % Allowed : 11.11 % Favored : 88.52 % 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 are not related in a simple way. whole: -0.88 (0.48), residues: 308 helix: 0.73 (0.48), residues: 112 sheet: -0.92 (0.56), residues: 78 loop : -1.54 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.009 0.001 TYR A 22 PHE 0.013 0.002 PHE A 369 TRP 0.010 0.002 TRP A 229 HIS 0.004 0.002 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 ( 4745) covalent geometry : angle 0.56715 / 0.34 ( 6826) hydrogen bonds : bond 0.04852 / 5.48 ( 165) hydrogen bonds : angle 4.13382 / 4.86 ( 412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.130 Fit side-chains REVERT: A 20 ASP cc_start: 0.7104 (m-30) cc_final: 0.6686 (t0) REVERT: A 56 VAL cc_start: 0.6859 (p) cc_final: 0.6589 (t) REVERT: A 102 GLU cc_start: 0.7631 (pm20) cc_final: 0.7370 (pm20) outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.1128 time to fit residues: 6.7067 Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.178502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.142729 restraints weight = 6470.955| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.50 r_work: 0.3609 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4745 Z= 0.240 Angle : 0.643 9.284 6826 Z= 0.373 Chirality : 0.044 0.240 800 Planarity : 0.006 0.054 547 Dihedral : 25.812 178.826 1619 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.59 % Allowed : 11.48 % Favored : 85.93 % 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 are not related in a simple way. whole: -1.15 (0.47), residues: 308 helix: 0.38 (0.47), residues: 112 sheet: -1.02 (0.58), residues: 77 loop : -1.59 (0.58), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 96 TYR 0.015 0.002 TYR A 22 PHE 0.016 0.002 PHE A 369 TRP 0.004 0.002 TRP A 229 HIS 0.004 0.002 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.24 ( 4745) covalent geometry : angle 0.64343 / 0.37 ( 6826) hydrogen bonds : bond 0.05475 / 5.84 ( 165) hydrogen bonds : angle 4.29651 / 5.15 ( 412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.122 Fit side-chains REVERT: A 102 GLU cc_start: 0.7645 (pm20) cc_final: 0.7346 (pm20) REVERT: A 167 ARG cc_start: 0.4551 (mtt180) cc_final: 0.4004 (mtt180) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 0.1276 time to fit residues: 9.2214 Evaluate side-chains 62 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 204 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.4173 > 50: distance: 43 - 48: 16.504 distance: 48 - 49: 14.665 distance: 49 - 50: 17.093 distance: 49 - 52: 24.397 distance: 50 - 51: 29.538 distance: 50 - 54: 13.247 distance: 52 - 53: 21.048 distance: 54 - 55: 12.109 distance: 55 - 56: 5.685 distance: 55 - 58: 7.976 distance: 56 - 57: 19.194 distance: 56 - 65: 8.172 distance: 58 - 59: 12.694 distance: 59 - 60: 3.902 distance: 60 - 61: 5.974 distance: 61 - 62: 3.949 distance: 62 - 63: 6.062 distance: 62 - 64: 5.954 distance: 65 - 66: 6.378 distance: 66 - 67: 9.739 distance: 66 - 69: 14.308 distance: 67 - 68: 15.696 distance: 67 - 77: 4.229 distance: 70 - 71: 3.528 distance: 70 - 72: 4.212 distance: 71 - 73: 5.827 distance: 72 - 74: 4.743 distance: 73 - 75: 5.262 distance: 75 - 76: 5.972 distance: 77 - 78: 9.832 distance: 78 - 79: 16.338 distance: 78 - 81: 12.198 distance: 79 - 80: 27.382 distance: 79 - 88: 10.426 distance: 81 - 82: 3.789 distance: 82 - 83: 7.866 distance: 82 - 84: 5.303 distance: 83 - 85: 5.706 distance: 84 - 86: 4.247 distance: 85 - 87: 7.882 distance: 86 - 87: 9.909 distance: 88 - 89: 29.226 distance: 89 - 90: 12.713 distance: 89 - 92: 21.962 distance: 90 - 91: 14.627 distance: 90 - 102: 49.432 distance: 92 - 93: 12.449 distance: 93 - 94: 11.565 distance: 93 - 95: 7.536 distance: 94 - 96: 9.240 distance: 95 - 97: 10.701 distance: 95 - 98: 10.437 distance: 96 - 97: 5.575 distance: 97 - 99: 6.856 distance: 98 - 100: 7.966 distance: 99 - 101: 8.135 distance: 100 - 101: 11.472 distance: 102 - 103: 42.960 distance: 103 - 104: 18.493 distance: 103 - 106: 23.659 distance: 104 - 105: 15.713 distance: 104 - 110: 8.721 distance: 106 - 107: 14.098 distance: 107 - 108: 10.892 distance: 107 - 109: 6.319 distance: 110 - 111: 19.374 distance: 110 - 116: 4.890 distance: 111 - 112: 7.365 distance: 111 - 114: 12.201 distance: 112 - 113: 27.716 distance: 112 - 117: 3.557 distance: 114 - 115: 9.299 distance: 115 - 116: 10.421 distance: 117 - 118: 7.193 distance: 118 - 119: 7.590 distance: 118 - 121: 6.754 distance: 119 - 120: 9.261 distance: 119 - 123: 7.733 distance: 120 - 164: 10.269 distance: 121 - 122: 9.862 distance: 123 - 124: 12.985 distance: 124 - 125: 10.522 distance: 124 - 127: 4.911 distance: 125 - 126: 11.893 distance: 125 - 130: 10.146 distance: 127 - 128: 4.801 distance: 127 - 129: 12.408 distance: 130 - 131: 10.913 distance: 130 - 154: 10.409 distance: 131 - 132: 22.715 distance: 132 - 133: 9.000 distance: 132 - 134: 17.196 distance: 133 - 151: 23.636