Starting phenix.real_space_refine on Fri Jul 3 02:43:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9d_65771/07_2026/9w9d_65771.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9d_65771/07_2026/9w9d_65771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w9d_65771/07_2026/9w9d_65771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9d_65771/07_2026/9w9d_65771.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w9d_65771/07_2026/9w9d_65771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9d_65771/07_2026/9w9d_65771.map" } resolution = 4.4 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= 0.032 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 148 5.49 5 S 18 5.16 5 C 6757 2.51 5 N 2026 2.21 5 O 2530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 11479 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 8301 Classifications: {'peptide': 1014} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 987} Chain breaks: 3 Chain: "B" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 761 Classifications: {'DNA': 37} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 36} Chain: "C" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 286 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 2131 Classifications: {'RNA': 100} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 49, 'rna3p_pyr': 40} Link IDs: {'rna2p': 11, 'rna3p': 88} Time building chain proxies: 2.37, per 1000 atoms: 0.21 Number of scatterers: 11479 At special positions: 0 Unit cell: (121.362, 118.14, 111.696, 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 18 16.00 P 148 15.00 O 2530 8.00 N 2026 7.00 C 6757 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: 0.93 Conformation dependent library (CDL) restraints added in 395.3 milliseconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1928 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 54.6% alpha, 8.4% beta 58 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.358A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 removed outlier: 4.310A pdb=" N HIS A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 103 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.544A pdb=" N GLU A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.648A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.782A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 381 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.958A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 3.937A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.594A pdb=" N VAL A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.988A pdb=" N MET A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.280A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.640A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 719 through 727 Processing helix chain 'A' and resid 730 through 751 Processing helix chain 'A' and resid 927 through 940 Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.163A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 999 removed outlier: 4.270A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.572A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 3.549A pdb=" N LYS A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 3.854A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 removed outlier: 3.514A pdb=" N ASN A1295 " --> pdb=" O LEU A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1317 removed outlier: 4.231A pdb=" N THR A1314 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR A1316 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 956 removed outlier: 6.385A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 760 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 19 " --> pdb=" O GLY A 8 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A1093 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 9.955A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A1348 " --> pdb=" O LEU A1203 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.951A pdb=" N LYS A 528 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 5.721A pdb=" N LYS A1156 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU A1150 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1324 through 1326 384 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 148 hydrogen bonds 292 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2566 1.33 - 1.45: 3170 1.45 - 1.57: 5947 1.57 - 1.69: 296 1.69 - 1.81: 34 Bond restraints: 12013 Sorted by residual: bond pdb=" C3' DG C 3 " pdb=" C2' DG C 3 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DA C 13 " pdb=" C2' DA C 13 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DC B 16 " pdb=" C2' DC B 16 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.82e+00 bond pdb=" C3' DG B 7 " pdb=" C2' DG B 7 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.31e+00 bond pdb=" C3' DG B 12 " pdb=" C2' DG B 12 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.27e+00 ... (remaining 12008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 16381 1.49 - 2.98: 469 2.98 - 4.48: 23 4.48 - 5.97: 4 5.97 - 7.46: 2 Bond angle restraints: 16879 Sorted by residual: angle pdb=" O4' DG B 23 " pdb=" C4' DG B 23 " pdb=" C3' DG B 23 " ideal model delta sigma weight residual 106.00 102.58 3.42 6.00e-01 2.78e+00 3.25e+01 angle pdb=" O4' DG B 18 " pdb=" C4' DG B 18 " pdb=" C3' DG B 18 " ideal model delta sigma weight residual 106.00 102.82 3.18 6.00e-01 2.78e+00 2.80e+01 angle pdb=" O4' DT B 19 " pdb=" C4' DT B 19 " pdb=" C3' DT B 19 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.64e+01 angle pdb=" O4' DC B 29 " pdb=" C4' DC B 29 " pdb=" C3' DC B 29 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.30e+01 angle pdb=" O4' DC B 30 " pdb=" C4' DC B 30 " pdb=" C3' DC B 30 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.27e+01 ... (remaining 16874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.00: 6832 32.00 - 64.00: 384 64.00 - 96.00: 32 96.00 - 128.00: 0 128.00 - 160.00: 1 Dihedral angle restraints: 7249 sinusoidal: 4271 harmonic: 2978 Sorted by residual: dihedral pdb=" C4' DG B 7 " pdb=" C3' DG B 7 " pdb=" O3' DG B 7 " pdb=" P DA B 8 " ideal model delta sinusoidal sigma weight residual 220.00 60.00 160.00 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" CA ASP A 288 " pdb=" CB ASP A 288 " pdb=" CG ASP A 288 " pdb=" OD1 ASP A 288 " ideal model delta sinusoidal sigma weight residual -30.00 -86.95 56.95 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CG ARG A1359 " pdb=" CD ARG A1359 " pdb=" NE ARG A1359 " pdb=" CZ ARG A1359 " ideal model delta sinusoidal sigma weight residual -180.00 -135.45 -44.55 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 7246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1328 0.030 - 0.059: 402 0.059 - 0.089: 136 0.089 - 0.119: 82 0.119 - 0.148: 5 Chirality restraints: 1953 Sorted by residual: chirality pdb=" P DA B 8 " pdb=" OP1 DA B 8 " pdb=" OP2 DA B 8 " pdb=" O5' DA B 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" C3' DG C 4 " pdb=" C4' DG C 4 " pdb=" O3' DG C 4 " pdb=" C2' DG C 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" C3' DG B 7 " pdb=" C4' DG B 7 " pdb=" O3' DG B 7 " pdb=" C2' DG B 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.61 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 1950 not shown) Planarity restraints: 1596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U D 99 " -0.030 2.00e-02 2.50e+03 1.45e-02 4.73e+00 pdb=" N1 U D 99 " 0.027 2.00e-02 2.50e+03 pdb=" C2 U D 99 " 0.006 2.00e-02 2.50e+03 pdb=" O2 U D 99 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U D 99 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U D 99 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U D 99 " -0.010 2.00e-02 2.50e+03 pdb=" C5 U D 99 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U D 99 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C D 98 " -0.021 2.00e-02 2.50e+03 1.09e-02 2.66e+00 pdb=" N1 C D 98 " 0.023 2.00e-02 2.50e+03 pdb=" C2 C D 98 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C D 98 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C D 98 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C D 98 " -0.006 2.00e-02 2.50e+03 pdb=" N4 C D 98 " -0.003 2.00e-02 2.50e+03 pdb=" C5 C D 98 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C D 98 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1228 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A1229 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1229 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1229 " -0.022 5.00e-02 4.00e+02 ... (remaining 1593 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 5 2.02 - 2.74: 988 2.74 - 3.46: 16308 3.46 - 4.18: 29983 4.18 - 4.90: 46910 Nonbonded interactions: 94194 Sorted by model distance: nonbonded pdb=" NZ LYS A 742 " pdb=" OP1 C D 69 " model vdw 1.296 3.120 nonbonded pdb=" NH1 ARG A 71 " pdb=" N4 C D 20 " model vdw 1.352 3.200 nonbonded pdb=" O GLY A 582 " pdb=" C4' DT B 33 " model vdw 1.378 3.470 nonbonded pdb=" CG GLN A 695 " pdb=" O3' DC B 35 " model vdw 1.380 3.440 nonbonded pdb=" O GLY A 582 " pdb=" C5' DT B 33 " model vdw 1.841 3.440 ... (remaining 94189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.430 Find NCS groups from input model: 0.030 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.003 0.040 12013 Z= 0.283 Angle : 0.562 7.461 16879 Z= 0.454 Chirality : 0.037 0.148 1953 Planarity : 0.003 0.040 1596 Dihedral : 16.944 159.996 5321 Min Nonbonded Distance : 1.296 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.81 (0.27), residues: 1006 helix: 2.10 (0.23), residues: 501 sheet: 1.03 (0.61), residues: 69 loop : 0.23 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 71 TYR 0.011 0.001 TYR A1242 PHE 0.013 0.001 PHE A 970 TRP 0.011 0.002 TRP A 464 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.28 (12013) covalent geometry : angle 0.56156 / 0.45 (16879) hydrogen bonds : bond 0.14342 / 9.73 ( 532) hydrogen bonds : angle 5.35664 / 3.91 ( 1414) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 TYR cc_start: 0.8891 (t80) cc_final: 0.8458 (t80) REVERT: A 662 LEU cc_start: 0.9049 (mt) cc_final: 0.8799 (mp) REVERT: A 744 VAL cc_start: 0.9741 (t) cc_final: 0.9473 (t) REVERT: A 954 LYS cc_start: 0.9421 (mttt) cc_final: 0.9038 (mmtm) REVERT: A 1317 ASN cc_start: 0.8712 (m-40) cc_final: 0.8407 (m-40) REVERT: A 1357 GLU cc_start: 0.7878 (pt0) cc_final: 0.7579 (pm20) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1370 time to fit residues: 31.3187 Evaluate side-chains 99 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 50.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 30.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS A 739 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.059838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.050930 restraints weight = 137666.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.052138 restraints weight = 76383.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.052896 restraints weight = 52274.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.053447 restraints weight = 40339.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.053824 restraints weight = 33193.983| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12013 Z= 0.181 Angle : 0.625 10.536 16879 Z= 0.351 Chirality : 0.041 0.207 1953 Planarity : 0.005 0.063 1596 Dihedral : 19.292 161.651 3169 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: 1.32 (0.26), residues: 1006 helix: 1.63 (0.23), residues: 517 sheet: 1.67 (0.65), residues: 59 loop : -0.11 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 661 TYR 0.018 0.002 TYR A1201 PHE 0.016 0.002 PHE A 98 TRP 0.013 0.001 TRP A 659 HIS 0.015 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.18 (12013) covalent geometry : angle 0.62475 / 0.35 (16879) hydrogen bonds : bond 0.05556 / 3.79 ( 532) hydrogen bonds : angle 4.66118 / 3.35 ( 1414) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.9783 (tt) cc_final: 0.9267 (tp) REVERT: A 86 PHE cc_start: 0.9456 (m-80) cc_final: 0.9121 (m-10) REVERT: A 155 TYR cc_start: 0.9427 (t80) cc_final: 0.9226 (t80) REVERT: A 450 TYR cc_start: 0.9159 (p90) cc_final: 0.8675 (p90) REVERT: A 662 LEU cc_start: 0.9625 (mt) cc_final: 0.9409 (mt) REVERT: A 694 MET cc_start: 0.9468 (tpt) cc_final: 0.9026 (tpp) REVERT: A 1134 PHE cc_start: 0.9502 (m-80) cc_final: 0.9168 (m-80) REVERT: A 1204 PHE cc_start: 0.9735 (m-80) cc_final: 0.9088 (m-80) REVERT: A 1317 ASN cc_start: 0.9067 (m-40) cc_final: 0.8862 (m-40) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1095 time to fit residues: 15.6240 Evaluate side-chains 82 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.1371 > 50: distance: 10 - 34: 4.826 distance: 34 - 35: 9.529 distance: 35 - 36: 13.770 distance: 35 - 38: 13.004 distance: 36 - 37: 8.349 distance: 36 - 42: 17.719 distance: 38 - 39: 12.350 distance: 39 - 40: 4.711 distance: 39 - 41: 7.024 distance: 42 - 43: 19.050 distance: 42 - 48: 16.171 distance: 43 - 44: 18.277 distance: 43 - 46: 19.135 distance: 44 - 45: 22.844 distance: 44 - 49: 3.347 distance: 46 - 47: 19.708 distance: 47 - 48: 25.176 distance: 49 - 50: 6.698 distance: 50 - 51: 3.712 distance: 50 - 53: 13.990 distance: 51 - 52: 14.793 distance: 51 - 58: 10.575 distance: 53 - 54: 4.919 distance: 54 - 55: 21.606 distance: 55 - 57: 6.752 distance: 58 - 59: 4.597 distance: 59 - 60: 9.233 distance: 59 - 62: 8.126 distance: 60 - 61: 9.533 distance: 60 - 67: 3.674 distance: 61 - 97: 13.708 distance: 62 - 63: 6.178 distance: 63 - 64: 11.631 distance: 64 - 65: 13.888 distance: 65 - 66: 7.477 distance: 68 - 69: 5.623 distance: 68 - 71: 5.706 distance: 69 - 70: 5.913 distance: 69 - 79: 6.515 distance: 70 - 105: 17.915 distance: 72 - 73: 3.539 distance: 77 - 78: 8.294 distance: 80 - 81: 4.879 distance: 80 - 83: 3.255 distance: 81 - 82: 14.194 distance: 81 - 88: 9.094 distance: 82 - 116: 20.396 distance: 83 - 84: 5.019 distance: 85 - 86: 4.711 distance: 86 - 87: 4.225 distance: 88 - 89: 5.340 distance: 89 - 90: 5.240 distance: 89 - 92: 3.807 distance: 90 - 91: 7.415 distance: 90 - 97: 8.360 distance: 92 - 93: 6.178 distance: 93 - 94: 4.918 distance: 94 - 95: 4.118 distance: 94 - 96: 3.367 distance: 97 - 98: 5.905 distance: 98 - 99: 7.086 distance: 98 - 101: 5.468 distance: 99 - 100: 10.881 distance: 99 - 105: 7.994 distance: 102 - 104: 8.219 distance: 105 - 106: 5.086 distance: 106 - 107: 5.208 distance: 106 - 109: 6.516 distance: 107 - 108: 26.222 distance: 107 - 116: 16.412 distance: 109 - 110: 9.029 distance: 110 - 111: 7.202 distance: 110 - 112: 5.276 distance: 111 - 113: 3.403 distance: 112 - 114: 5.095 distance: 113 - 115: 3.678 distance: 114 - 115: 3.028 distance: 116 - 117: 15.008 distance: 117 - 118: 11.267 distance: 117 - 120: 13.446 distance: 118 - 119: 13.604 distance: 118 - 127: 7.559 distance: 120 - 121: 7.553 distance: 121 - 122: 7.337 distance: 121 - 123: 10.160 distance: 122 - 124: 8.697 distance: 123 - 125: 7.121 distance: 124 - 126: 5.518 distance: 125 - 126: 3.166