Starting phenix.real_space_refine on Thu Jul 2 12:55:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8blo_16110/07_2026/8blo_16110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8blo_16110/07_2026/8blo_16110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8blo_16110/07_2026/8blo_16110.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8blo_16110/07_2026/8blo_16110.cif" model { file = "/net/cci-nas-00/data/ceres_data/8blo_16110/07_2026/8blo_16110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8blo_16110/07_2026/8blo_16110.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8blo_16110/07_2026/8blo_16110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8blo_16110/07_2026/8blo_16110.map" } resolution = 2.9 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= 0.003 sd= 0.152 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 3 5.49 5 S 51 5.16 5 C 5724 2.51 5 N 1239 2.21 5 O 1470 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8487 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2646 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 19, 'TRANS': 332} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 177 Unusual residues: {'LMN': 5, 'PLD': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 506 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'PLD:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Restraints were copied for chains: C, B Time building chain proxies: 1.85, per 1000 atoms: 0.22 Number of scatterers: 8487 At special positions: 0 Unit cell: (97.58, 103.32, 72.98, 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 51 16.00 P 3 15.00 O 1470 8.00 N 1239 7.00 C 5724 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: 0.69 Conformation dependent library (CDL) restraints added in 192.4 milliseconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 75.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 93 through 98 removed outlier: 3.579A pdb=" N TYR A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 134 through 149 Processing helix chain 'A' and resid 149 through 170 Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 215 through 229 removed outlier: 4.474A pdb=" N VAL A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 251 Processing helix chain 'A' and resid 278 through 292 removed outlier: 4.003A pdb=" N ILE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 298 through 313 Processing helix chain 'A' and resid 313 through 334 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.811A pdb=" N LEU A 352 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 391 Processing helix chain 'A' and resid 399 through 412 Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.966A pdb=" N VAL A 427 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'C' and resid 93 through 98 removed outlier: 3.579A pdb=" N TYR C 97 " --> pdb=" O LYS C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 113 through 128 Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 134 through 149 Processing helix chain 'C' and resid 149 through 170 Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 215 through 229 removed outlier: 4.474A pdb=" N VAL C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 251 Processing helix chain 'C' and resid 278 through 292 removed outlier: 4.003A pdb=" N ILE C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) Proline residue: C 287 - end of helix Processing helix chain 'C' and resid 298 through 313 Processing helix chain 'C' and resid 313 through 334 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 347 through 358 removed outlier: 3.809A pdb=" N LEU C 352 " --> pdb=" O TYR C 348 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER C 353 " --> pdb=" O ASN C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 391 Processing helix chain 'C' and resid 399 through 412 Processing helix chain 'C' and resid 423 through 427 removed outlier: 3.967A pdb=" N VAL C 427 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.579A pdb=" N TYR B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 110 Processing helix chain 'B' and resid 113 through 128 Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 134 through 149 Processing helix chain 'B' and resid 149 through 170 Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 215 through 229 removed outlier: 4.474A pdb=" N VAL B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 251 Processing helix chain 'B' and resid 278 through 292 removed outlier: 4.003A pdb=" N ILE B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Proline residue: B 287 - end of helix Processing helix chain 'B' and resid 298 through 313 Processing helix chain 'B' and resid 313 through 334 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 347 through 358 removed outlier: 3.809A pdb=" N LEU B 352 " --> pdb=" O TYR B 348 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 391 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.967A pdb=" N VAL B 427 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 531 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1209 1.31 - 1.43: 2317 1.43 - 1.56: 4957 1.56 - 1.68: 124 1.68 - 1.81: 78 Bond restraints: 8685 Sorted by residual: bond pdb=" CB PLD A1001 " pdb=" O3 PLD A1001 " ideal model delta sigma weight residual 1.325 1.432 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" CB PLD B1001 " pdb=" O3 PLD B1001 " ideal model delta sigma weight residual 1.325 1.432 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" CB PLD C1001 " pdb=" O3 PLD C1001 " ideal model delta sigma weight residual 1.325 1.432 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C' PLD A1001 " pdb=" O2 PLD A1001 " ideal model delta sigma weight residual 1.331 1.407 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C' PLD C1001 " pdb=" O2 PLD C1001 " ideal model delta sigma weight residual 1.331 1.407 -0.076 2.00e-02 2.50e+03 1.44e+01 ... (remaining 8680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 11563 3.45 - 6.90: 209 6.90 - 10.35: 15 10.35 - 13.80: 0 13.80 - 17.25: 3 Bond angle restraints: 11790 Sorted by residual: angle pdb=" O3P PLD C1001 " pdb=" P PLD C1001 " pdb=" O4P PLD C1001 " ideal model delta sigma weight residual 92.85 110.10 -17.25 3.00e+00 1.11e-01 3.30e+01 angle pdb=" O3P PLD A1001 " pdb=" P PLD A1001 " pdb=" O4P PLD A1001 " ideal model delta sigma weight residual 92.85 110.09 -17.24 3.00e+00 1.11e-01 3.30e+01 angle pdb=" O3P PLD B1001 " pdb=" P PLD B1001 " pdb=" O4P PLD B1001 " ideal model delta sigma weight residual 92.85 110.07 -17.22 3.00e+00 1.11e-01 3.30e+01 angle pdb=" C VAL A 235 " pdb=" N PHE A 236 " pdb=" CA PHE A 236 " ideal model delta sigma weight residual 121.54 128.36 -6.82 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C VAL B 235 " pdb=" N PHE B 236 " pdb=" CA PHE B 236 " ideal model delta sigma weight residual 121.54 128.31 -6.77 1.91e+00 2.74e-01 1.26e+01 ... (remaining 11785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.22: 4818 32.22 - 64.45: 186 64.45 - 96.67: 21 96.67 - 128.89: 6 128.89 - 161.11: 9 Dihedral angle restraints: 5040 sinusoidal: 1989 harmonic: 3051 Sorted by residual: dihedral pdb=" OB PLD A1001 " pdb=" CB PLD A1001 " pdb=" O3 PLD A1001 " pdb=" C3 PLD A1001 " ideal model delta sinusoidal sigma weight residual -7.40 153.71 -161.11 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" OB PLD B1001 " pdb=" CB PLD B1001 " pdb=" O3 PLD B1001 " pdb=" C3 PLD B1001 " ideal model delta sinusoidal sigma weight residual -7.40 153.71 -161.11 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" OB PLD C1001 " pdb=" CB PLD C1001 " pdb=" O3 PLD C1001 " pdb=" C3 PLD C1001 " ideal model delta sinusoidal sigma weight residual -7.40 153.62 -161.02 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 5037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1045 0.048 - 0.097: 277 0.097 - 0.145: 31 0.145 - 0.193: 0 0.193 - 0.241: 3 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C2 PLD A1001 " pdb=" C1 PLD A1001 " pdb=" C3 PLD A1001 " pdb=" O2 PLD A1001 " both_signs ideal model delta sigma weight residual False -2.34 -2.58 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C2 PLD C1001 " pdb=" C1 PLD C1001 " pdb=" C3 PLD C1001 " pdb=" O2 PLD C1001 " both_signs ideal model delta sigma weight residual False -2.34 -2.58 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C2 PLD B1001 " pdb=" C1 PLD B1001 " pdb=" C3 PLD B1001 " pdb=" O2 PLD B1001 " both_signs ideal model delta sigma weight residual False -2.34 -2.58 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1353 not shown) Planarity restraints: 1383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 279 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO B 280 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 280 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 280 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 279 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO C 280 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 280 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 280 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 279 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 280 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 280 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 280 " 0.027 5.00e-02 4.00e+02 ... (remaining 1380 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2715 2.84 - 3.36: 8344 3.36 - 3.87: 14980 3.87 - 4.39: 18813 4.39 - 4.90: 30406 Nonbonded interactions: 75258 Sorted by model distance: nonbonded pdb=" O GLU A 339 " pdb=" OG1 THR A 343 " model vdw 2.328 3.040 nonbonded pdb=" O GLU C 339 " pdb=" OG1 THR C 343 " model vdw 2.328 3.040 nonbonded pdb=" O GLU B 339 " pdb=" OG1 THR B 343 " model vdw 2.328 3.040 nonbonded pdb=" OG1 THR C 164 " pdb=" O HOH C1101 " model vdw 2.435 3.040 nonbonded pdb=" OG SER C 353 " pdb=" SG CYS C 379 " model vdw 2.441 3.400 ... (remaining 75253 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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: 2.030 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.280 Find NCS groups from input model: 0.070 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:5.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 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 : 0.008 0.107 8685 Z= 0.391 Angle : 0.955 17.245 11790 Z= 0.425 Chirality : 0.042 0.241 1356 Planarity : 0.005 0.048 1383 Dihedral : 18.691 161.115 3084 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.86 % Favored : 96.86 % Rotamer: Outliers : 0.98 % Allowed : 3.44 % Favored : 95.57 % 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: -1.47 (0.24), residues: 1050 helix: -0.73 (0.17), residues: 753 sheet: None (None), residues: 0 loop : -1.21 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 174 TYR 0.013 0.001 TYR A 184 PHE 0.016 0.002 PHE C 361 TRP 0.006 0.001 TRP B 300 HIS 0.003 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.39 ( 8685) covalent geometry : angle 0.95461 / 0.43 (11790) hydrogen bonds : bond 0.10732 / 7.39 ( 531) hydrogen bonds : angle 4.49842 / 3.24 ( 1584) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.290 Fit side-chains REVERT: B 387 SER cc_start: 0.8367 (t) cc_final: 0.8135 (m) outliers start: 8 outliers final: 1 residues processed: 101 average time/residue: 0.3417 time to fit residues: 37.9820 Evaluate side-chains 79 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 ASN C 415 ASN B 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.110061 restraints weight = 9202.447| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.33 r_work: 0.2967 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8685 Z= 0.124 Angle : 0.545 8.545 11790 Z= 0.267 Chirality : 0.040 0.140 1356 Planarity : 0.005 0.052 1383 Dihedral : 20.293 176.716 1501 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.21 % Allowed : 8.24 % Favored : 89.54 % 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: 0.24 (0.25), residues: 1050 helix: 0.59 (0.18), residues: 753 sheet: None (None), residues: 0 loop : -0.72 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 174 TYR 0.011 0.001 TYR A 184 PHE 0.016 0.001 PHE B 361 TRP 0.011 0.001 TRP C 108 HIS 0.002 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.12 ( 8685) covalent geometry : angle 0.54535 / 0.27 (11790) hydrogen bonds : bond 0.03768 / 2.52 ( 531) hydrogen bonds : angle 3.75312 / 2.76 ( 1584) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.227 Fit side-chains REVERT: A 230 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7992 (mmmt) REVERT: A 387 SER cc_start: 0.8527 (t) cc_final: 0.8223 (m) REVERT: C 119 ILE cc_start: 0.8349 (mt) cc_final: 0.7943 (mp) REVERT: C 408 ILE cc_start: 0.8572 (mt) cc_final: 0.8210 (mt) REVERT: B 230 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8193 (mmmt) REVERT: B 387 SER cc_start: 0.8508 (t) cc_final: 0.8285 (m) REVERT: B 408 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8063 (mt) outliers start: 18 outliers final: 3 residues processed: 97 average time/residue: 0.3066 time to fit residues: 32.7934 Evaluate side-chains 87 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 408 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 ASN A 416 ASN C 415 ASN B 415 ASN B 416 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.135595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.109557 restraints weight = 9179.369| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.33 r_work: 0.2952 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8685 Z= 0.136 Angle : 0.563 8.508 11790 Z= 0.273 Chirality : 0.041 0.163 1356 Planarity : 0.005 0.053 1383 Dihedral : 18.428 174.415 1500 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.85 % Allowed : 10.09 % Favored : 88.07 % 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: 0.81 (0.26), residues: 1050 helix: 0.93 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -0.30 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 174 TYR 0.013 0.001 TYR A 184 PHE 0.024 0.002 PHE B 378 TRP 0.007 0.001 TRP C 108 HIS 0.003 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 8685) covalent geometry : angle 0.56275 / 0.27 (11790) hydrogen bonds : bond 0.03757 / 2.51 ( 531) hydrogen bonds : angle 3.75803 / 2.76 ( 1584) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.178 Fit side-chains REVERT: A 230 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8030 (mmmt) REVERT: A 387 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.8212 (m) REVERT: B 230 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8134 (mmmt) REVERT: B 387 SER cc_start: 0.8472 (t) cc_final: 0.8253 (m) outliers start: 15 outliers final: 4 residues processed: 90 average time/residue: 0.3322 time to fit residues: 32.8476 Evaluate side-chains 88 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 230 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 65.699 > 50: distance: 41 - 62: 9.276 distance: 48 - 73: 33.810 distance: 52 - 81: 16.518 distance: 56 - 62: 9.587 distance: 57 - 87: 13.589 distance: 62 - 63: 11.234 distance: 63 - 64: 16.058 distance: 63 - 66: 10.988 distance: 64 - 65: 8.157 distance: 64 - 73: 59.800 distance: 66 - 67: 17.805 distance: 67 - 68: 26.872 distance: 67 - 69: 16.054 distance: 68 - 70: 15.348 distance: 69 - 71: 16.787 distance: 71 - 72: 24.292 distance: 73 - 74: 14.801 distance: 74 - 75: 32.734 distance: 74 - 77: 25.634 distance: 75 - 76: 12.048 distance: 75 - 81: 12.502 distance: 78 - 80: 39.052 distance: 81 - 82: 12.845 distance: 82 - 83: 4.520 distance: 82 - 85: 25.236 distance: 83 - 84: 10.175 distance: 83 - 87: 21.296 distance: 85 - 86: 31.073 distance: 87 - 88: 9.899 distance: 88 - 91: 31.480 distance: 89 - 90: 20.799 distance: 89 - 93: 16.729 distance: 90 - 116: 38.806 distance: 91 - 92: 18.390 distance: 93 - 94: 7.710 distance: 93 - 99: 18.259 distance: 94 - 95: 6.469 distance: 94 - 97: 12.931 distance: 95 - 96: 25.074 distance: 95 - 100: 8.365 distance: 96 - 122: 6.592 distance: 97 - 98: 18.833 distance: 98 - 99: 31.650 distance: 100 - 101: 21.570 distance: 101 - 102: 19.828 distance: 101 - 104: 14.007 distance: 102 - 103: 11.418 distance: 102 - 108: 9.478 distance: 103 - 130: 28.408 distance: 104 - 105: 20.110 distance: 105 - 106: 4.563 distance: 105 - 107: 18.493 distance: 108 - 109: 6.658 distance: 109 - 110: 18.714 distance: 110 - 111: 16.323 distance: 110 - 116: 4.218 distance: 111 - 140: 18.061 distance: 112 - 113: 28.541 distance: 112 - 114: 12.380 distance: 113 - 115: 19.759 distance: 116 - 117: 8.771 distance: 117 - 118: 13.563 distance: 117 - 120: 21.389 distance: 118 - 119: 10.483 distance: 118 - 122: 7.501 distance: 119 - 145: 16.402 distance: 120 - 121: 34.165 distance: 122 - 123: 10.466 distance: 123 - 124: 7.576 distance: 123 - 126: 8.464 distance: 124 - 125: 11.081 distance: 124 - 130: 10.049 distance: 125 - 150: 21.229 distance: 126 - 127: 8.025 distance: 127 - 128: 18.361 distance: 127 - 129: 39.292 distance: 130 - 131: 5.040 distance: 131 - 132: 12.363 distance: 131 - 134: 7.374 distance: 132 - 133: 6.881 distance: 132 - 140: 5.951 distance: 133 - 158: 10.260 distance: 134 - 135: 11.400 distance: 135 - 136: 7.931 distance: 135 - 137: 12.878 distance: 136 - 138: 15.509 distance: 137 - 139: 8.926 distance: 138 - 139: 11.985