Starting phenix.real_space_refine on Thu Jul 2 00:06:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k7b_62147/07_2026/9k7b_62147.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k7b_62147/07_2026/9k7b_62147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k7b_62147/07_2026/9k7b_62147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k7b_62147/07_2026/9k7b_62147.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k7b_62147/07_2026/9k7b_62147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k7b_62147/07_2026/9k7b_62147.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.090 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: 6 Type Number sf(0) Gaussians S 36 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 3048 2.51 5 N 664 2.21 5 O 772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 4522 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4333 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 27, 'TRANS': 516} Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 187 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Unusual residues: {'CLR': 5, 'TAU': 4} Classifications: {'undetermined': 9, 'water': 19} Link IDs: {None: 26} Chain breaks: 2 Time building chain proxies: 1.20, per 1000 atoms: 0.27 Number of scatterers: 4522 At special positions: 0 Unit cell: (82.49, 65.7, 87.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 36 16.00 Na 1 11.00 O 772 8.00 N 664 7.00 C 3048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 149.4 milliseconds 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 82.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.522A pdb=" N LEU A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.971A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 4.019A pdb=" N PHE A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.765A pdb=" N GLU A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 153 removed outlier: 3.516A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.631A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.862A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'A' and resid 245 through 266 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.993A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 286' Processing helix chain 'A' and resid 287 through 303 removed outlier: 4.153A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.500A pdb=" N SER A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.853A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 removed outlier: 4.538A pdb=" N ALA A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.509A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 424 through 447 removed outlier: 4.046A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.773A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 539 through 568 removed outlier: 4.072A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL A 557 " --> pdb=" O SER A 553 " (cutoff:3.500A) Proline residue: A 558 - end of helix Processing helix chain 'A' and resid 571 through 581 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 287 hydrogen bonds defined for protein. 855 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: 0.69 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 643 1.32 - 1.44: 1388 1.44 - 1.57: 2574 1.57 - 1.69: 0 1.69 - 1.82: 50 Bond restraints: 4655 Sorted by residual: bond pdb=" C PRO A 118 " pdb=" O PRO A 118 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.26e-02 6.30e+03 1.29e+01 bond pdb=" CA MET A 381 " pdb=" C MET A 381 " ideal model delta sigma weight residual 1.527 1.558 -0.030 1.02e-02 9.61e+03 8.87e+00 bond pdb=" CA SER A 365 " pdb=" C SER A 365 " ideal model delta sigma weight residual 1.530 1.496 0.034 1.14e-02 7.69e+03 8.73e+00 bond pdb=" C CYS A 71 " pdb=" O CYS A 71 " ideal model delta sigma weight residual 1.236 1.203 0.033 1.15e-02 7.56e+03 8.21e+00 bond pdb=" CA GLY A 295 " pdb=" C GLY A 295 " ideal model delta sigma weight residual 1.517 1.484 0.032 1.14e-02 7.69e+03 8.06e+00 ... (remaining 4650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 6264 4.49 - 8.98: 103 8.98 - 13.47: 10 13.47 - 17.95: 1 17.95 - 22.44: 1 Bond angle restraints: 6379 Sorted by residual: angle pdb=" N ALA A 462 " pdb=" CA ALA A 462 " pdb=" C ALA A 462 " ideal model delta sigma weight residual 111.07 119.90 -8.83 1.07e+00 8.73e-01 6.82e+01 angle pdb=" O1 TAU A 701 " pdb=" S TAU A 701 " pdb=" O2 TAU A 701 " ideal model delta sigma weight residual 113.04 90.60 22.44 3.00e+00 1.11e-01 5.60e+01 angle pdb=" N LEU A 278 " pdb=" CA LEU A 278 " pdb=" C LEU A 278 " ideal model delta sigma weight residual 111.36 119.10 -7.74 1.09e+00 8.42e-01 5.05e+01 angle pdb=" N VAL A 510 " pdb=" CA VAL A 510 " pdb=" C VAL A 510 " ideal model delta sigma weight residual 111.62 116.99 -5.37 7.90e-01 1.60e+00 4.63e+01 angle pdb=" N VAL A 64 " pdb=" CA VAL A 64 " pdb=" C VAL A 64 " ideal model delta sigma weight residual 110.72 117.17 -6.45 1.01e+00 9.80e-01 4.07e+01 ... (remaining 6374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.78: 2710 23.78 - 47.56: 114 47.56 - 71.34: 29 71.34 - 95.11: 3 95.11 - 118.89: 5 Dihedral angle restraints: 2861 sinusoidal: 1293 harmonic: 1568 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual 93.00 179.49 -86.49 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" C1 CLR A 707 " pdb=" C2 CLR A 707 " pdb=" C3 CLR A 707 " pdb=" O1 CLR A 707 " ideal model delta sinusoidal sigma weight residual 180.04 61.15 118.89 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C10 CLR A 707 " pdb=" C1 CLR A 707 " pdb=" C2 CLR A 707 " pdb=" C3 CLR A 707 " ideal model delta sinusoidal sigma weight residual -56.83 61.06 -117.89 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 2858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 455 0.078 - 0.155: 168 0.155 - 0.233: 61 0.233 - 0.310: 27 0.310 - 0.388: 3 Chirality restraints: 714 Sorted by residual: chirality pdb=" CA LEU A 278 " pdb=" N LEU A 278 " pdb=" C LEU A 278 " pdb=" CB LEU A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA PHE A 474 " pdb=" N PHE A 474 " pdb=" C PHE A 474 " pdb=" CB PHE A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA TYR A 137 " pdb=" N TYR A 137 " pdb=" C TYR A 137 " pdb=" CB TYR A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 711 not shown) Planarity restraints: 743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 374 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.72e+00 pdb=" N PRO A 375 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 92 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 93 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 512 " 0.040 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO A 513 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 513 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 513 " 0.034 5.00e-02 4.00e+02 ... (remaining 740 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 14 2.41 - 3.03: 2947 3.03 - 3.65: 6947 3.65 - 4.28: 11641 4.28 - 4.90: 18703 Nonbonded interactions: 40252 Sorted by model distance: nonbonded pdb=" O PHE A 392 " pdb=" CD1 LEU A 396 " model vdw 1.784 3.460 nonbonded pdb=" NH1 ARG A 66 " pdb=" OD1 ASP A 459 " model vdw 2.030 3.120 nonbonded pdb=" N1 TAU A 703 " pdb=" O1 TAU A 704 " model vdw 2.175 3.120 nonbonded pdb=" CG1 VAL A 182 " pdb=" CE3 TRP A 183 " model vdw 2.195 3.760 nonbonded pdb=" CG LEU A 52 " pdb=" CE1 PHE A 58 " model vdw 2.229 3.770 ... (remaining 40247 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.090 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:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 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 : 0.013 0.664 4657 Z= 1.152 Angle : 1.403 22.442 6381 Z= 0.871 Chirality : 0.102 0.388 714 Planarity : 0.008 0.074 743 Dihedral : 14.676 118.892 1866 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.71 % Allowed : 6.42 % Favored : 91.86 % 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: 1.92 (0.35), residues: 542 helix: 2.20 (0.25), residues: 386 sheet: None (None), residues: 0 loop : -1.16 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 66 TYR 0.018 0.002 TYR A 69 PHE 0.018 0.002 PHE A 392 TRP 0.017 0.002 TRP A 113 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00845 / 0.62 ( 4655) covalent geometry : angle 1.40188 / 0.87 ( 6379) SS BOND : bond 0.00413 / 0.22 ( 1) SS BOND : angle 3.33827 / 1.80 ( 2) hydrogen bonds : bond 0.18057 / 11.61 ( 287) hydrogen bonds : angle 6.40464 / 4.63 ( 855) Misc. bond : bond 0.66383 / 34.94 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.161 Fit side-chains REVERT: A 113 TRP cc_start: 0.6943 (m100) cc_final: 0.6594 (m100) REVERT: A 161 HIS cc_start: 0.8358 (m-70) cc_final: 0.8103 (m-70) REVERT: A 197 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6596 (mt-10) REVERT: A 200 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6699 (mt-10) REVERT: A 275 LYS cc_start: 0.5752 (ttmt) cc_final: 0.5228 (mttp) REVERT: A 289 GLN cc_start: 0.7225 (pt0) cc_final: 0.6458 (mt0) REVERT: A 309 MET cc_start: 0.7636 (mmt) cc_final: 0.7325 (mmt) REVERT: A 325 ASP cc_start: 0.6862 (m-30) cc_final: 0.6566 (m-30) REVERT: A 402 SER cc_start: 0.7277 (m) cc_final: 0.6799 (p) REVERT: A 494 ASP cc_start: 0.7647 (t0) cc_final: 0.7407 (t0) REVERT: A 504 MET cc_start: 0.7072 (mmt) cc_final: 0.6418 (mmt) outliers start: 8 outliers final: 2 residues processed: 102 average time/residue: 0.3367 time to fit residues: 36.3864 Evaluate side-chains 62 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 375 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN A 154 GLN A 164 HIS A 333 ASN A 355 GLN A 567 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.157823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.119046 restraints weight = 4859.444| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.80 r_work: 0.3174 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4657 Z= 0.162 Angle : 0.705 10.136 6381 Z= 0.342 Chirality : 0.047 0.239 714 Planarity : 0.005 0.040 743 Dihedral : 10.583 69.141 929 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.36 % Allowed : 11.99 % Favored : 85.65 % 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: 1.63 (0.35), residues: 542 helix: 1.79 (0.25), residues: 395 sheet: None (None), residues: 0 loop : -0.88 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 324 TYR 0.019 0.001 TYR A 69 PHE 0.028 0.002 PHE A 58 TRP 0.015 0.002 TRP A 470 HIS 0.008 0.002 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 4655) covalent geometry : angle 0.68870 / 0.33 ( 6379) SS BOND : bond 0.01112 / 0.59 ( 1) SS BOND : angle 8.45920 / 4.61 ( 2) hydrogen bonds : bond 0.05277 / 3.38 ( 287) hydrogen bonds : angle 4.93421 / 3.52 ( 855) Misc. bond : bond 0.00954 / 0.50 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.102 Fit side-chains REVERT: A 113 TRP cc_start: 0.7646 (m100) cc_final: 0.7339 (m100) REVERT: A 176 MET cc_start: 0.6789 (mmm) cc_final: 0.6430 (mmm) REVERT: A 200 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8168 (mt-10) REVERT: A 275 LYS cc_start: 0.7500 (ttmt) cc_final: 0.6904 (mtmt) REVERT: A 401 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7430 (t70) REVERT: A 504 MET cc_start: 0.8212 (mmt) cc_final: 0.7835 (mmt) REVERT: A 506 TYR cc_start: 0.6886 (m-10) cc_final: 0.5840 (t80) outliers start: 11 outliers final: 3 residues processed: 73 average time/residue: 0.4719 time to fit residues: 35.9027 Evaluate side-chains 56 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 486 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.155454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115418 restraints weight = 4654.949| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.82 r_work: 0.3183 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4657 Z= 0.145 Angle : 0.637 17.500 6381 Z= 0.302 Chirality : 0.045 0.216 714 Planarity : 0.004 0.034 743 Dihedral : 9.247 59.682 926 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.93 % Allowed : 14.99 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.36), residues: 542 helix: 1.74 (0.26), residues: 397 sheet: None (None), residues: 0 loop : -0.91 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 583 TYR 0.019 0.001 TYR A 69 PHE 0.019 0.002 PHE A 191 TRP 0.012 0.001 TRP A 113 HIS 0.004 0.002 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 4655) covalent geometry : angle 0.63378 / 0.30 ( 6379) SS BOND : bond 0.00684 / 0.36 ( 1) SS BOND : angle 3.53961 / 1.95 ( 2) hydrogen bonds : bond 0.04836 / 3.10 ( 287) hydrogen bonds : angle 4.78131 / 3.41 ( 855) Misc. bond : bond 0.00847 / 0.45 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.209 Fit side-chains REVERT: A 113 TRP cc_start: 0.7824 (m100) cc_final: 0.7491 (m100) REVERT: A 200 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8301 (mt-10) REVERT: A 275 LYS cc_start: 0.7633 (ttmt) cc_final: 0.7039 (mtmt) REVERT: A 284 ARG cc_start: 0.7720 (mmt180) cc_final: 0.7004 (tmt170) REVERT: A 289 GLN cc_start: 0.8289 (pt0) cc_final: 0.7693 (tt0) REVERT: A 504 MET cc_start: 0.8309 (mmt) cc_final: 0.7920 (mmt) REVERT: A 506 TYR cc_start: 0.7003 (m-10) cc_final: 0.6025 (t80) outliers start: 9 outliers final: 4 residues processed: 70 average time/residue: 0.4099 time to fit residues: 30.2861 Evaluate side-chains 61 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 SER 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: 52.0065 > 50: distance: 18 - 46: 6.986 distance: 26 - 54: 8.371 distance: 31 - 32: 3.249 distance: 31 - 34: 4.071 distance: 32 - 41: 3.705 distance: 33 - 62: 10.565 distance: 34 - 35: 3.404 distance: 35 - 36: 4.116 distance: 35 - 37: 5.242 distance: 36 - 38: 5.588 distance: 37 - 39: 3.815 distance: 38 - 40: 4.639 distance: 39 - 40: 6.373 distance: 41 - 42: 3.323 distance: 42 - 45: 4.040 distance: 43 - 44: 10.482 distance: 43 - 46: 7.159 distance: 44 - 70: 37.714 distance: 47 - 48: 5.533 distance: 47 - 50: 4.632 distance: 48 - 54: 7.896 distance: 49 - 77: 16.755 distance: 50 - 51: 6.708 distance: 51 - 52: 4.329 distance: 52 - 53: 8.767 distance: 54 - 55: 6.170 distance: 55 - 56: 4.836 distance: 55 - 58: 5.683 distance: 56 - 57: 3.995 distance: 57 - 85: 17.043 distance: 58 - 59: 7.928 distance: 59 - 60: 7.789 distance: 59 - 61: 11.866 distance: 62 - 63: 5.298 distance: 63 - 64: 7.535 distance: 63 - 66: 9.284 distance: 64 - 65: 18.601 distance: 64 - 70: 33.780 distance: 65 - 93: 19.909 distance: 66 - 67: 10.285 distance: 67 - 68: 11.648 distance: 67 - 69: 9.613 distance: 70 - 71: 34.776 distance: 71 - 72: 16.429 distance: 71 - 74: 11.473 distance: 72 - 73: 10.881 distance: 73 - 100: 16.627 distance: 74 - 75: 6.835 distance: 74 - 76: 11.054 distance: 77 - 78: 12.092 distance: 78 - 79: 3.619 distance: 78 - 81: 6.971 distance: 79 - 80: 4.121 distance: 79 - 85: 6.704 distance: 80 - 111: 4.705 distance: 81 - 82: 8.403 distance: 82 - 83: 11.370 distance: 82 - 84: 11.697 distance: 85 - 86: 3.297 distance: 86 - 87: 4.244 distance: 86 - 89: 6.970 distance: 87 - 88: 3.280 distance: 87 - 93: 7.284 distance: 88 - 115: 3.581 distance: 89 - 90: 7.472 distance: 90 - 91: 4.428 distance: 90 - 92: 5.769 distance: 93 - 94: 3.590 distance: 94 - 97: 5.341 distance: 95 - 96: 5.933 distance: 95 - 100: 3.762 distance: 96 - 123: 7.381 distance: 97 - 98: 3.053 distance: 97 - 99: 7.204 distance: 101 - 102: 3.079 distance: 101 - 104: 3.910 distance: 102 - 103: 4.180 distance: 104 - 105: 3.360 distance: 106 - 107: 3.062 distance: 107 - 108: 4.751 distance: 108 - 109: 4.593 distance: 140 - 147: 3.277