Starting phenix.real_space_refine on Sat Jul 4 20:58:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jl2_61576/07_2026/9jl2_61576.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jl2_61576/07_2026/9jl2_61576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jl2_61576/07_2026/9jl2_61576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jl2_61576/07_2026/9jl2_61576.map" model { file = "/net/cci-nas-00/data/ceres_data/9jl2_61576/07_2026/9jl2_61576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jl2_61576/07_2026/9jl2_61576.cif" } resolution = 3.0 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= 0.009 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 P 133 5.49 5 S 18 5.16 5 C 7146 2.51 5 N 2101 2.21 5 O 2605 1.98 5 H 10804 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 22807 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 885 Classifications: {'DNA': 28} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 320 Classifications: {'DNA': 10} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 18511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 18511 Classifications: {'peptide': 1125} Link IDs: {'PTRANS': 30, 'TRANS': 1094} Chain breaks: 2 Chain: "B" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 3091 Classifications: {'RNA': 96} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 84} Time building chain proxies: 2.84, per 1000 atoms: 0.12 Number of scatterers: 22807 At special positions: 0 Unit cell: (89.1, 128.7, 122.76, 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) S 18 16.00 P 133 15.00 O 2605 8.00 N 2101 7.00 C 7146 6.00 H 10804 1.00 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: 2.24 Conformation dependent library (CDL) restraints added in 544.4 milliseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 8 sheets defined 54.3% alpha, 7.6% beta 49 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 59 through 86 removed outlier: 3.586A pdb=" N PHE A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.515A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 removed outlier: 3.746A pdb=" N GLU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 103 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.559A pdb=" N HIS A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.822A 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 180 through 194 removed outlier: 3.596A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.920A pdb=" N ALA A 214 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 270 through 282 removed outlier: 4.199A pdb=" N ASP A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 286 through 306 removed outlier: 3.733A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 342 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 removed outlier: 3.571A pdb=" N PHE A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A 377 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.887A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 411 through 427 removed outlier: 3.938A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.827A pdb=" N ASP A 435 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 512 through 522 removed outlier: 3.657A pdb=" N VAL A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 Processing helix chain 'A' and resid 541 through 553 removed outlier: 3.675A pdb=" N ASP A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 removed outlier: 4.366A pdb=" N GLU A 566 " --> pdb=" O LYS A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.695A pdb=" N ASP A 618 " --> pdb=" O ASP A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 643 removed outlier: 5.283A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 642 " --> pdb=" O TYR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 654 removed outlier: 3.828A pdb=" N ARG A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 703 through 715 Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 734 through 749 Processing helix chain 'A' and resid 927 through 939 removed outlier: 3.918A pdb=" N GLN A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 970 removed outlier: 4.280A pdb=" N LYS A 968 " --> pdb=" O SER A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 999 removed outlier: 4.185A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 998 " --> pdb=" O GLY A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1087 removed outlier: 3.597A pdb=" N LYS A1085 " --> pdb=" O ALA A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.538A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 3.585A 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 1280 removed outlier: 4.383A pdb=" N ILE A1270 " --> pdb=" O LEU A1266 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A1271 " --> pdb=" O ASP A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1310 removed outlier: 3.540A pdb=" N ASN A1308 " --> pdb=" O GLU A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1315 removed outlier: 3.577A pdb=" N THR A1314 " --> pdb=" O HIS A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.836A pdb=" N LEU A1343 " --> pdb=" O THR A1339 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP A1344 " --> pdb=" O LYS A1340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1339 through 1344' Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.236A pdb=" N ALA A 50 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.828A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA5, first strand: chain 'A' and resid 759 through 760 removed outlier: 6.670A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1163 removed outlier: 3.581A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1163 removed outlier: 3.578A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1324 through 1326 394 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 122 hydrogen bonds 240 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10802 1.03 - 1.23: 80 1.23 - 1.42: 5503 1.42 - 1.62: 6891 1.62 - 1.81: 34 Bond restraints: 23310 Sorted by residual: bond pdb=" ND2 ASN A 121 " pdb="HD22 ASN A 121 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" ND2 ASN A 121 " pdb="HD21 ASN A 121 " ideal model delta sigma weight residual 0.860 0.977 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" N9 A B 51 " pdb=" C4 A B 51 " ideal model delta sigma weight residual 1.374 1.352 0.022 6.00e-03 2.78e+04 1.34e+01 bond pdb=" C3' DT C 11 " pdb=" C2' DT C 11 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" N1 DC C -2 " pdb=" C6 DC C -2 " ideal model delta sigma weight residual 1.367 1.347 0.020 6.00e-03 2.78e+04 1.13e+01 ... (remaining 23305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 40583 1.52 - 3.03: 1493 3.03 - 4.55: 104 4.55 - 6.06: 16 6.06 - 7.58: 1 Bond angle restraints: 42197 Sorted by residual: angle pdb=" O4' DG C 3 " pdb=" C4' DG C 3 " pdb=" C3' DG C 3 " ideal model delta sigma weight residual 106.00 102.87 3.13 6.00e-01 2.78e+00 2.73e+01 angle pdb=" O4' DT C 6 " pdb=" C4' DT C 6 " pdb=" C3' DT C 6 " ideal model delta sigma weight residual 106.00 103.03 2.97 6.00e-01 2.78e+00 2.46e+01 angle pdb=" O4' DC C 7 " pdb=" C4' DC C 7 " pdb=" C3' DC C 7 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.14e+01 angle pdb=" N3 DT C -4 " pdb=" C4 DT C -4 " pdb=" O4 DT C -4 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT C -3 " pdb=" C4 DT C -3 " pdb=" O4 DT C -3 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 42192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 9266 17.94 - 35.87: 894 35.87 - 53.81: 392 53.81 - 71.74: 172 71.74 - 89.68: 36 Dihedral angle restraints: 10760 sinusoidal: 6886 harmonic: 3874 Sorted by residual: dihedral pdb=" CA SER A1216 " pdb=" C SER A1216 " pdb=" N ALA A1217 " pdb=" CA ALA A1217 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA GLU A1243 " pdb=" C GLU A1243 " pdb=" N LYS A1244 " pdb=" CA LYS A1244 " ideal model delta harmonic sigma weight residual 180.00 153.02 26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA GLU A 505 " pdb=" C GLU A 505 " pdb=" N LYS A 506 " pdb=" CA LYS A 506 " ideal model delta harmonic sigma weight residual -180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 10757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1530 0.045 - 0.090: 378 0.090 - 0.135: 81 0.135 - 0.180: 25 0.180 - 0.225: 7 Chirality restraints: 2021 Sorted by residual: chirality pdb=" C3' DC C 7 " pdb=" C4' DC C 7 " pdb=" O3' DC C 7 " pdb=" C2' DC C 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C3' DT C 6 " pdb=" C4' DT C 6 " pdb=" O3' DT C 6 " pdb=" C2' DT C 6 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C3' DT C 4 " pdb=" C4' DT C 4 " pdb=" O3' DT C 4 " pdb=" C2' DT C 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2018 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 121 " 0.195 2.00e-02 2.50e+03 1.97e-01 5.80e+02 pdb=" CG ASN A 121 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 121 " -0.186 2.00e-02 2.50e+03 pdb=" ND2 ASN A 121 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 121 " -0.282 2.00e-02 2.50e+03 pdb="HD22 ASN A 121 " 0.283 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A1089 " -0.071 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO A1090 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO A1090 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A1090 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 377 " -0.049 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO A 378 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.040 5.00e-02 4.00e+02 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 574 2.11 - 2.73: 38010 2.73 - 3.35: 64007 3.35 - 3.98: 83029 3.98 - 4.60: 129030 Nonbonded interactions: 314650 Sorted by model distance: nonbonded pdb=" OE1 GLU A 427 " pdb=" H GLU A 427 " model vdw 1.482 2.450 nonbonded pdb="HH22 ARG A 400 " pdb=" OD2 ASP A 406 " model vdw 1.525 2.450 nonbonded pdb="HH11 ARG A 967 " pdb=" OD1 ASP A 986 " model vdw 1.533 2.450 nonbonded pdb=" HH TYR A 373 " pdb=" O LEU A 398 " model vdw 1.552 2.450 nonbonded pdb=" HG SER A 512 " pdb=" OE2 GLU A 617 " model vdw 1.552 2.450 ... (remaining 314645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.040 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: 0.140 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 21.230 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.006 0.094 12506 Z= 0.425 Angle : 0.694 7.577 17471 Z= 0.505 Chirality : 0.045 0.225 2021 Planarity : 0.005 0.106 1740 Dihedral : 18.629 89.678 5447 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.06 % Favored : 92.85 % Rotamer: Outliers : 0.40 % Allowed : 11.82 % Favored : 87.79 % 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: -1.89 (0.24), residues: 1119 helix: -0.82 (0.22), residues: 516 sheet: -2.07 (0.51), residues: 90 loop : -1.45 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 40 TYR 0.014 0.002 TYR A1336 PHE 0.027 0.002 PHE A1080 TRP 0.010 0.002 TRP A 476 HIS 0.008 0.002 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.43 (12506) covalent geometry : angle 0.69401 / 0.51 (17471) hydrogen bonds : bond 0.18472 / 21.00 ( 508) hydrogen bonds : angle 7.10092 / 9.09 ( 1359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 219 time to evaluate : 0.391 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: 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 outliers start: 4 outliers final: 3 residues processed: 222 average time/residue: 1.1127 time to fit residues: 267.4365 Evaluate side-chains 107 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 1310 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN A 489 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.122438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.083754 restraints weight = 74883.418| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.88 r_work: 0.3285 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 12506 Z= 0.255 Angle : 0.673 7.086 17471 Z= 0.388 Chirality : 0.043 0.188 2021 Planarity : 0.005 0.070 1740 Dihedral : 18.847 91.029 3082 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 2.28 % Allowed : 18.07 % Favored : 79.64 % 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: -1.67 (0.24), residues: 1119 helix: -0.61 (0.21), residues: 547 sheet: -2.02 (0.43), residues: 117 loop : -1.31 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 753 TYR 0.029 0.002 TYR A 286 PHE 0.021 0.002 PHE A1258 TRP 0.008 0.001 TRP A 476 HIS 0.006 0.001 HIS A 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.25 (12506) covalent geometry : angle 0.67283 / 0.39 (17471) hydrogen bonds : bond 0.06458 / 7.22 ( 508) hydrogen bonds : angle 5.27712 / 6.64 ( 1359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.342 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ASP cc_start: 0.8271 (t0) cc_final: 0.8060 (t0) REVERT: A 933 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8471 (tm-30) REVERT: A 963 VAL cc_start: 0.8602 (t) cc_final: 0.8391 (m) outliers start: 23 outliers final: 4 residues processed: 127 average time/residue: 1.0377 time to fit residues: 143.9810 Evaluate side-chains 92 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 26 optimal weight: 30.0000 chunk 103 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.121647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.083717 restraints weight = 74374.818| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.80 r_work: 0.3280 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12506 Z= 0.206 Angle : 0.592 6.815 17471 Z= 0.344 Chirality : 0.040 0.175 2021 Planarity : 0.004 0.060 1740 Dihedral : 18.775 92.778 3076 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 2.38 % Allowed : 18.37 % Favored : 79.25 % 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: -1.45 (0.24), residues: 1119 helix: -0.42 (0.21), residues: 538 sheet: -1.88 (0.44), residues: 117 loop : -1.20 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 753 TYR 0.015 0.001 TYR A 155 PHE 0.025 0.002 PHE A 256 TRP 0.007 0.001 TRP A 18 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.21 (12506) covalent geometry : angle 0.59229 / 0.34 (17471) hydrogen bonds : bond 0.05726 / 6.38 ( 508) hydrogen bonds : angle 4.91378 / 6.16 ( 1359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.682 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ASP cc_start: 0.8345 (t0) cc_final: 0.8120 (t0) REVERT: A 648 MET cc_start: 0.6765 (tmm) cc_final: 0.6378 (tmm) REVERT: A 933 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8565 (tm130) outliers start: 24 outliers final: 8 residues processed: 110 average time/residue: 0.8912 time to fit residues: 109.6476 Evaluate side-chains 90 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 30.0000 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 92 optimal weight: 0.0970 chunk 111 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.121214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.082535 restraints weight = 75291.326| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.85 r_work: 0.3270 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12506 Z= 0.204 Angle : 0.580 7.559 17471 Z= 0.333 Chirality : 0.040 0.192 2021 Planarity : 0.004 0.056 1740 Dihedral : 18.733 94.853 3076 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.52 % Favored : 93.39 % Rotamer: Outliers : 1.59 % Allowed : 18.47 % Favored : 79.94 % 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: -1.36 (0.24), residues: 1119 helix: -0.39 (0.21), residues: 542 sheet: -1.89 (0.44), residues: 117 loop : -1.08 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.015 0.001 TYR A 155 PHE 0.015 0.002 PHE A 478 TRP 0.006 0.001 TRP A 18 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (12506) covalent geometry : angle 0.58005 / 0.33 (17471) hydrogen bonds : bond 0.05075 / 5.64 ( 508) hydrogen bonds : angle 4.69633 / 5.92 ( 1359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.516 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 104 average time/residue: 0.9639 time to fit residues: 110.9229 Evaluate side-chains 90 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1099 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 105 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.120635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.082075 restraints weight = 75179.520| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.85 r_work: 0.3262 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12506 Z= 0.209 Angle : 0.569 5.812 17471 Z= 0.329 Chirality : 0.039 0.170 2021 Planarity : 0.004 0.052 1740 Dihedral : 18.727 96.238 3076 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.43 % Favored : 93.48 % Rotamer: Outliers : 1.89 % Allowed : 19.46 % Favored : 78.65 % 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: -1.30 (0.24), residues: 1119 helix: -0.31 (0.21), residues: 543 sheet: -1.83 (0.45), residues: 117 loop : -1.10 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 661 TYR 0.015 0.001 TYR A 155 PHE 0.016 0.001 PHE A 478 TRP 0.006 0.001 TRP A 18 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 (12506) covalent geometry : angle 0.56877 / 0.33 (17471) hydrogen bonds : bond 0.04957 / 5.50 ( 508) hydrogen bonds : angle 4.58801 / 5.79 ( 1359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.498 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 938 ARG cc_start: 0.8410 (mmm-85) cc_final: 0.7831 (tpp-160) outliers start: 19 outliers final: 10 residues processed: 98 average time/residue: 0.9689 time to fit residues: 104.7519 Evaluate side-chains 90 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1099 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 2 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.120534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.082062 restraints weight = 75433.017| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.81 r_work: 0.3267 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12506 Z= 0.181 Angle : 0.550 6.675 17471 Z= 0.318 Chirality : 0.039 0.180 2021 Planarity : 0.004 0.048 1740 Dihedral : 18.714 97.405 3076 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 1.99 % Allowed : 19.36 % Favored : 78.65 % 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: -1.16 (0.25), residues: 1119 helix: -0.17 (0.22), residues: 544 sheet: -1.78 (0.46), residues: 113 loop : -1.08 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 63 TYR 0.015 0.001 TYR A 155 PHE 0.015 0.001 PHE A 478 TRP 0.005 0.001 TRP A 18 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (12506) covalent geometry : angle 0.55045 / 0.32 (17471) hydrogen bonds : bond 0.04682 / 5.19 ( 508) hydrogen bonds : angle 4.43067 / 5.59 ( 1359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.527 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: symmetry clash revert: symmetry clash REVERT: A 661 ARG cc_start: 0.8610 (mmm-85) cc_final: 0.8050 (mpp80) REVERT: A 938 ARG cc_start: 0.8423 (mmm-85) cc_final: 0.7835 (tpp-160) outliers start: 20 outliers final: 10 residues processed: 97 average time/residue: 0.9307 time to fit residues: 100.4843 Evaluate side-chains 87 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1310 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 52.7232 > 50: distance: 315 - 353: 12.011 distance: 324 - 374: 25.954 distance: 337 - 353: 15.468 distance: 353 - 354: 22.511 distance: 353 - 365: 5.583 distance: 354 - 355: 20.165 distance: 354 - 357: 13.862 distance: 354 - 366: 31.614 distance: 355 - 356: 19.463 distance: 355 - 374: 25.962 distance: 357 - 358: 16.643 distance: 357 - 367: 28.902 distance: 357 - 368: 31.067 distance: 358 - 359: 11.043 distance: 358 - 360: 10.673 distance: 359 - 369: 5.275 distance: 360 - 362: 4.599 distance: 360 - 370: 8.213 distance: 361 - 363: 3.299 distance: 361 - 371: 4.232 distance: 362 - 363: 11.142 distance: 362 - 372: 4.877 distance: 363 - 364: 13.570 distance: 364 - 373: 11.922 distance: 374 - 375: 27.117 distance: 374 - 378: 37.360 distance: 375 - 376: 4.998 distance: 375 - 379: 30.580 distance: 375 - 380: 13.623 distance: 376 - 377: 16.748 distance: 376 - 381: 11.618 distance: 381 - 382: 7.551 distance: 381 - 385: 42.070 distance: 382 - 383: 20.770 distance: 382 - 386: 20.091 distance: 382 - 387: 18.460 distance: 383 - 384: 19.249 distance: 383 - 388: 20.313 distance: 388 - 389: 11.514 distance: 388 - 399: 32.776 distance: 389 - 390: 14.983 distance: 389 - 392: 11.445 distance: 389 - 400: 23.107 distance: 390 - 391: 21.981 distance: 390 - 408: 13.719 distance: 392 - 393: 8.309 distance: 392 - 401: 10.088 distance: 392 - 402: 7.672 distance: 393 - 394: 13.261 distance: 393 - 395: 5.574 distance: 394 - 396: 6.215 distance: 394 - 403: 4.039 distance: 396 - 398: 6.776 distance: 396 - 405: 6.208 distance: 397 - 406: 4.113 distance: 398 - 407: 3.174 distance: 408 - 409: 17.106 distance: 408 - 416: 15.936 distance: 409 - 410: 35.724 distance: 409 - 412: 15.562 distance: 409 - 417: 18.770 distance: 410 - 411: 29.328 distance: 410 - 420: 45.029 distance: 412 - 413: 6.293 distance: 412 - 418: 10.364 distance: 412 - 419: 8.616 distance: 413 - 414: 9.051 distance: 413 - 415: 12.706 distance: 420 - 421: 49.974 distance: 420 - 426: 35.193 distance: 421 - 422: 31.910 distance: 421 - 424: 20.638 distance: 421 - 427: 27.432 distance: 422 - 423: 13.461 distance: 422 - 431: 11.489 distance: 424 - 425: 7.212 distance: 424 - 428: 7.024 distance: 424 - 429: 11.322 distance: 425 - 430: 4.961 distance: 431 - 432: 10.338 distance: 431 - 437: 5.087 distance: 432 - 433: 14.964 distance: 432 - 435: 8.317 distance: 432 - 438: 13.891 distance: 433 - 434: 15.572 distance: 433 - 445: 17.976 distance: 435 - 436: 9.146 distance: 435 - 439: 17.510 distance: 435 - 440: 12.487 distance: 436 - 437: 8.825 distance: 436 - 441: 10.055 distance: 436 - 442: 9.253 distance: 437 - 443: 14.892 distance: 437 - 444: 18.710 distance: 445 - 446: 8.860 distance: 445 - 452: 12.922 distance: 446 - 447: 7.555 distance: 446 - 449: 19.902 distance: 446 - 453: 15.300 distance: 447 - 448: 18.918 distance: 447 - 459: 13.678 distance: 449 - 450: 16.539 distance: 449 - 451: 20.489 distance: 449 - 454: 24.699 distance: 450 - 455: 10.643 distance: 451 - 456: 4.176 distance: 451 - 457: 8.001 distance: 451 - 458: 11.683 distance: 459 - 460: 22.902 distance: 459 - 466: 32.862 distance: 460 - 461: 11.103 distance: 460 - 463: 12.841 distance: 460 - 467: 12.355 distance: 461 - 462: 9.098 distance: 461 - 475: 15.805 distance: 463 - 464: 21.266 distance: 463 - 465: 19.504 distance: 463 - 468: 21.334 distance: 464 - 469: 17.254 distance: 464 - 470: 10.543 distance: 464 - 471: 12.313 distance: 465 - 472: 20.059 distance: 465 - 473: 21.053 distance: 465 - 474: 17.971 distance: 475 - 476: 10.578 distance: 475 - 480: 27.402 distance: 476 - 477: 17.100 distance: 476 - 479: 6.535 distance: 476 - 481: 23.516 distance: 477 - 478: 22.459 distance: 477 - 485: 21.853 distance: 479 - 482: 16.600 distance: 479 - 483: 15.701 distance: 479 - 484: 11.233