Starting phenix.real_space_refine on Tue Mar 3 12:20:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nen_49328/03_2026/9nen_49328.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nen_49328/03_2026/9nen_49328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nen_49328/03_2026/9nen_49328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nen_49328/03_2026/9nen_49328.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nen_49328/03_2026/9nen_49328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nen_49328/03_2026/9nen_49328.map" } resolution = 3.5 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= 0.015 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 30 5.16 5 C 2521 2.51 5 N 675 2.21 5 O 721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3947 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3947 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain breaks: 3 Time building chain proxies: 0.84, per 1000 atoms: 0.21 Number of scatterers: 3947 At special positions: 0 Unit cell: (56.826, 79.695, 100.485, 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 30 16.00 O 721 8.00 N 675 7.00 C 2521 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: 0.28 Conformation dependent library (CDL) restraints added in 159.3 milliseconds 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 944 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 1 sheets defined 60.3% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 28 through 40 removed outlier: 3.598A pdb=" N LEU A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 59 through 66 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.752A pdb=" N ALA A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 121 through 135 Processing helix chain 'A' and resid 145 through 159 removed outlier: 3.516A pdb=" N ILE A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 169 removed outlier: 3.558A pdb=" N LEU A 166 " --> pdb=" O MET A 162 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 186 removed outlier: 3.885A pdb=" N LEU A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 205 removed outlier: 3.569A pdb=" N ILE A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 removed outlier: 4.030A pdb=" N GLU A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 237 removed outlier: 3.540A pdb=" N LEU A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 removed outlier: 4.185A pdb=" N VAL A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 245' Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 265 through 275 removed outlier: 3.655A pdb=" N ALA A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.737A pdb=" N SER A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 322 through 334 removed outlier: 4.209A pdb=" N GLY A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 360 removed outlier: 3.505A pdb=" N LYS A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 391 through 407 removed outlier: 3.651A pdb=" N MET A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A 404 " --> pdb=" O CYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 440 removed outlier: 4.099A pdb=" N ILE A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 478 through 491 removed outlier: 3.514A pdb=" N TYR A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 490 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.544A pdb=" N VAL A 529 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 47 removed outlier: 6.093A pdb=" N PHE A 464 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N CYS A 499 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A 466 " --> pdb=" O CYS A 499 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A 372 " --> pdb=" O ILE A 465 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE A 467 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 374 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE A 371 " --> pdb=" O TYR A 411 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL A 413 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU A 373 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE A 415 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL A 375 " --> pdb=" O PHE A 415 " (cutoff:3.500A) 165 hydrogen bonds defined for protein. 480 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: 0.40 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1271 1.34 - 1.46: 822 1.46 - 1.58: 1876 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4017 Sorted by residual: bond pdb=" CB LYS A 49 " pdb=" CG LYS A 49 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.74e-01 bond pdb=" CB GLU A 267 " pdb=" CG GLU A 267 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.10e-01 bond pdb=" CB ASP A 427 " pdb=" CG ASP A 427 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.06e-01 bond pdb=" N GLY A 476 " pdb=" CA GLY A 476 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 7.00e-01 bond pdb=" CA ILE A 48 " pdb=" C ILE A 48 " ideal model delta sigma weight residual 1.518 1.527 -0.008 1.13e-02 7.83e+03 5.33e-01 ... (remaining 4012 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 5276 1.30 - 2.59: 101 2.59 - 3.89: 24 3.89 - 5.18: 9 5.18 - 6.48: 4 Bond angle restraints: 5414 Sorted by residual: angle pdb=" CB LYS A 49 " pdb=" CG LYS A 49 " pdb=" CD LYS A 49 " ideal model delta sigma weight residual 111.30 117.78 -6.48 2.30e+00 1.89e-01 7.93e+00 angle pdb=" CA LYS A 49 " pdb=" CB LYS A 49 " pdb=" CG LYS A 49 " ideal model delta sigma weight residual 114.10 119.15 -5.05 2.00e+00 2.50e-01 6.38e+00 angle pdb=" N ALA A 474 " pdb=" CA ALA A 474 " pdb=" C ALA A 474 " ideal model delta sigma weight residual 108.19 111.40 -3.21 1.29e+00 6.01e-01 6.18e+00 angle pdb=" C PHE A 506 " pdb=" N THR A 507 " pdb=" CA THR A 507 " ideal model delta sigma weight residual 122.46 125.95 -3.49 1.41e+00 5.03e-01 6.13e+00 angle pdb=" CA ILE A 48 " pdb=" CB ILE A 48 " pdb=" CG1 ILE A 48 " ideal model delta sigma weight residual 110.40 113.81 -3.41 1.70e+00 3.46e-01 4.02e+00 ... (remaining 5409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 2019 17.52 - 35.04: 289 35.04 - 52.57: 114 52.57 - 70.09: 24 70.09 - 87.61: 5 Dihedral angle restraints: 2451 sinusoidal: 1000 harmonic: 1451 Sorted by residual: dihedral pdb=" CA LEU A 282 " pdb=" C LEU A 282 " pdb=" N ARG A 283 " pdb=" CA ARG A 283 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASN A 310 " pdb=" CB ASN A 310 " pdb=" CG ASN A 310 " pdb=" OD1 ASN A 310 " ideal model delta sinusoidal sigma weight residual -90.00 -153.83 63.83 2 2.00e+01 2.50e-03 9.67e+00 dihedral pdb=" CA GLU A 42 " pdb=" CB GLU A 42 " pdb=" CG GLU A 42 " pdb=" CD GLU A 42 " ideal model delta sinusoidal sigma weight residual -60.00 -118.09 58.09 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 383 0.029 - 0.057: 170 0.057 - 0.086: 45 0.086 - 0.114: 22 0.114 - 0.143: 6 Chirality restraints: 626 Sorted by residual: chirality pdb=" CG LEU A 341 " pdb=" CB LEU A 341 " pdb=" CD1 LEU A 341 " pdb=" CD2 LEU A 341 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA VAL A 424 " pdb=" N VAL A 424 " pdb=" C VAL A 424 " pdb=" CB VAL A 424 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE A 492 " pdb=" N ILE A 492 " pdb=" C ILE A 492 " pdb=" CB ILE A 492 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 623 not shown) Planarity restraints: 675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 320 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO A 321 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 27 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C VAL A 27 " 0.022 2.00e-02 2.50e+03 pdb=" O VAL A 27 " -0.008 2.00e-02 2.50e+03 pdb=" N THR A 28 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 510 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 511 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " -0.017 5.00e-02 4.00e+02 ... (remaining 672 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 137 2.72 - 3.26: 3892 3.26 - 3.81: 6221 3.81 - 4.35: 7893 4.35 - 4.90: 12757 Nonbonded interactions: 30900 Sorted by model distance: nonbonded pdb=" O ASP A 469 " pdb=" OG1 THR A 472 " model vdw 2.172 3.040 nonbonded pdb=" OG SER A 380 " pdb=" OD1 ASN A 470 " model vdw 2.283 3.040 nonbonded pdb=" O SER A 416 " pdb=" OG SER A 416 " model vdw 2.291 3.040 nonbonded pdb=" O LEU A 273 " pdb=" NZ LYS A 307 " model vdw 2.297 3.120 nonbonded pdb=" O THR A 459 " pdb=" OH TYR A 486 " model vdw 2.298 3.040 ... (remaining 30895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.100 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.260 Find NCS groups from input model: 0.010 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 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 : 0.002 0.030 4017 Z= 0.098 Angle : 0.526 6.479 5414 Z= 0.267 Chirality : 0.038 0.143 626 Planarity : 0.003 0.040 675 Dihedral : 19.478 87.609 1507 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.62 % Allowed : 40.60 % Favored : 57.77 % 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: -1.69 (0.37), residues: 493 helix: -0.90 (0.30), residues: 276 sheet: 0.69 (0.81), residues: 34 loop : -1.64 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.008 0.001 TYR A 486 PHE 0.006 0.001 PHE A 522 TRP 0.017 0.001 TRP A 206 HIS 0.002 0.000 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 4017) covalent geometry : angle 0.52594 ( 5414) hydrogen bonds : bond 0.28006 ( 165) hydrogen bonds : angle 8.76754 ( 480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.154 Fit side-chains REVERT: A 42 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6288 (mm-30) REVERT: A 74 ILE cc_start: 0.7381 (mm) cc_final: 0.7169 (mt) REVERT: A 233 GLU cc_start: 0.6073 (pt0) cc_final: 0.5342 (pm20) REVERT: A 267 GLU cc_start: 0.7281 (tp30) cc_final: 0.7073 (tp30) REVERT: A 275 GLU cc_start: 0.6815 (mp0) cc_final: 0.6558 (mp0) REVERT: A 311 GLU cc_start: 0.6467 (tp30) cc_final: 0.6055 (tp30) REVERT: A 315 LYS cc_start: 0.6430 (mtpt) cc_final: 0.6063 (mtpt) REVERT: A 519 MET cc_start: 0.7618 (mtp) cc_final: 0.7336 (mtt) outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 0.1126 time to fit residues: 11.8907 Evaluate side-chains 91 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 472 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.0670 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.139618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.127821 restraints weight = 5453.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.131393 restraints weight = 2848.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.133629 restraints weight = 1667.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.135139 restraints weight = 1058.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136048 restraints weight = 707.887| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4017 Z= 0.200 Angle : 0.592 7.374 5414 Z= 0.307 Chirality : 0.042 0.138 626 Planarity : 0.005 0.046 675 Dihedral : 5.424 44.364 537 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 7.42 % Allowed : 33.64 % Favored : 58.93 % 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: -1.28 (0.38), residues: 493 helix: -0.47 (0.30), residues: 285 sheet: 0.61 (0.89), residues: 33 loop : -1.60 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 32 TYR 0.021 0.002 TYR A 486 PHE 0.013 0.002 PHE A 39 TRP 0.012 0.002 TRP A 206 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 4017) covalent geometry : angle 0.59176 ( 5414) hydrogen bonds : bond 0.04221 ( 165) hydrogen bonds : angle 5.42091 ( 480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.090 Fit side-chains REVERT: A 42 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6648 (mm-30) REVERT: A 66 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.5747 (mt-10) REVERT: A 74 ILE cc_start: 0.7534 (mm) cc_final: 0.7195 (mt) REVERT: A 93 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7385 (mm) REVERT: A 233 GLU cc_start: 0.6339 (pt0) cc_final: 0.5466 (pm20) REVERT: A 288 MET cc_start: 0.7193 (mtm) cc_final: 0.6953 (mtt) REVERT: A 311 GLU cc_start: 0.6593 (tp30) cc_final: 0.6036 (tp30) REVERT: A 315 LYS cc_start: 0.6544 (mtpt) cc_final: 0.5884 (mtpt) REVERT: A 384 ARG cc_start: 0.7872 (tpp-160) cc_final: 0.7586 (mtp180) REVERT: A 451 MET cc_start: 0.7531 (mtm) cc_final: 0.7179 (mtm) REVERT: A 452 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6544 (mt) REVERT: A 519 MET cc_start: 0.7849 (mtp) cc_final: 0.7484 (mtt) outliers start: 32 outliers final: 14 residues processed: 123 average time/residue: 0.1003 time to fit residues: 14.4260 Evaluate side-chains 124 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 452 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/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-dev-5986/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/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-dev-5986/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-dev-5986/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-dev-5986/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-dev-5986/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-dev-5986/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-dev-5986/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-dev-5986/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-dev-5986/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-dev-5986/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-dev-5986/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-dev-5986/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-dev-5986/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-dev-5986/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-dev-5986/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-dev-5986/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.5568 > 50: distance: 65 - 85: 7.930 distance: 69 - 93: 10.769 distance: 73 - 77: 9.321 distance: 74 - 102: 13.339 distance: 78 - 79: 9.123 distance: 78 - 81: 8.842 distance: 79 - 80: 15.941 distance: 79 - 85: 5.879 distance: 80 - 114: 30.304 distance: 81 - 82: 4.726 distance: 82 - 83: 7.390 distance: 82 - 84: 11.694 distance: 85 - 86: 4.236 distance: 86 - 87: 7.846 distance: 86 - 89: 6.233 distance: 87 - 88: 10.625 distance: 87 - 93: 5.513 distance: 88 - 122: 18.992 distance: 89 - 90: 18.167 distance: 90 - 91: 17.702 distance: 90 - 92: 10.373 distance: 93 - 94: 8.337 distance: 94 - 95: 7.662 distance: 94 - 97: 8.987 distance: 95 - 96: 9.842 distance: 95 - 102: 21.663 distance: 96 - 131: 11.472 distance: 97 - 98: 11.908 distance: 98 - 99: 5.573 distance: 99 - 100: 13.218 distance: 100 - 101: 12.873 distance: 102 - 103: 10.039 distance: 103 - 104: 33.226 distance: 103 - 106: 14.463 distance: 104 - 105: 22.681 distance: 104 - 114: 15.663 distance: 105 - 136: 16.004 distance: 106 - 107: 9.085 distance: 107 - 108: 17.841 distance: 107 - 109: 6.649 distance: 108 - 110: 13.912 distance: 109 - 111: 9.390 distance: 111 - 112: 3.015 distance: 112 - 113: 4.774 distance: 114 - 115: 15.278 distance: 115 - 116: 26.449 distance: 115 - 118: 17.453 distance: 116 - 117: 23.933 distance: 116 - 122: 18.410 distance: 118 - 119: 15.215 distance: 119 - 120: 29.188 distance: 119 - 121: 22.568 distance: 122 - 123: 3.988 distance: 123 - 124: 9.995 distance: 123 - 126: 10.983 distance: 124 - 125: 7.077 distance: 124 - 131: 13.379 distance: 125 - 152: 32.168 distance: 126 - 127: 17.679 distance: 127 - 128: 15.596 distance: 128 - 129: 21.525 distance: 128 - 130: 11.473 distance: 131 - 132: 17.629 distance: 132 - 133: 5.724 distance: 132 - 135: 21.649 distance: 133 - 134: 7.597 distance: 133 - 136: 20.219 distance: 134 - 161: 28.078 distance: 136 - 137: 33.950 distance: 137 - 138: 34.792 distance: 137 - 140: 45.396 distance: 138 - 143: 7.251 distance: 140 - 141: 39.424 distance: 140 - 142: 4.064 distance: 143 - 144: 10.684 distance: 144 - 145: 17.545 distance: 144 - 147: 31.602 distance: 145 - 146: 5.361 distance: 145 - 152: 31.700 distance: 146 - 177: 24.080 distance: 147 - 148: 9.307 distance: 148 - 149: 30.202 distance: 149 - 150: 39.739 distance: 152 - 153: 14.518 distance: 153 - 154: 5.240 distance: 153 - 156: 4.173 distance: 154 - 155: 10.502 distance: 154 - 161: 5.293 distance: 156 - 157: 22.584 distance: 157 - 158: 43.980 distance: 158 - 159: 20.192 distance: 159 - 160: 8.077