Starting phenix.real_space_refine on Wed Mar 4 14:02:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fzt_29639/03_2026/8fzt_29639.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fzt_29639/03_2026/8fzt_29639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fzt_29639/03_2026/8fzt_29639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fzt_29639/03_2026/8fzt_29639.map" model { file = "/net/cci-nas-00/data/ceres_data/8fzt_29639/03_2026/8fzt_29639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fzt_29639/03_2026/8fzt_29639.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 149 5.49 5 S 22 5.16 5 C 8303 2.51 5 N 2436 2.21 5 O 3015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "E GLU 706": not complete - not flipped Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13925 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 10780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10780 Classifications: {'peptide': 1319} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 35, 'TRANS': 1283} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 803 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 17, 'rna3p_pyr': 20} Link IDs: {'rna2p': 1, 'rna3p': 36} Chain: "B" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1476 Classifications: {'RNA': 69} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 24} Link IDs: {'rna2p': 11, 'rna3p': 57} Chain: "C" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 616 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 2.92, per 1000 atoms: 0.21 Number of scatterers: 13925 At special positions: 0 Unit cell: (95.9, 128.1, 131.6, 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 22 16.00 P 149 15.00 O 3015 8.00 N 2436 7.00 C 8303 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: 1.27 Conformation dependent library (CDL) restraints added in 476.9 milliseconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2516 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 7 sheets defined 50.6% alpha, 6.0% beta 42 base pairs and 97 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'E' and resid 59 through 87 removed outlier: 4.112A pdb=" N ARG E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE E 79 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS E 80 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR E 81 " --> pdb=" O ASN E 77 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU E 82 " --> pdb=" O ARG E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.562A pdb=" N VAL E 93 " --> pdb=" O MET E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.578A pdb=" N ARG E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 101 " --> pdb=" O PHE E 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 96 through 101' Processing helix chain 'E' and resid 122 through 132 removed outlier: 3.922A pdb=" N VAL E 126 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA E 127 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N TYR E 128 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 145 removed outlier: 4.213A pdb=" N LEU E 138 " --> pdb=" O THR E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 164 removed outlier: 3.779A pdb=" N ILE E 154 " --> pdb=" O ASP E 150 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE E 164 " --> pdb=" O HIS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 196 Processing helix chain 'E' and resid 207 through 213 removed outlier: 3.668A pdb=" N ILE E 211 " --> pdb=" O ASP E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 229 removed outlier: 3.703A pdb=" N GLN E 228 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU E 229 " --> pdb=" O LEU E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 247 Processing helix chain 'E' and resid 253 through 257 removed outlier: 3.650A pdb=" N PHE E 256 " --> pdb=" O LYS E 253 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP E 257 " --> pdb=" O SER E 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 253 through 257' Processing helix chain 'E' and resid 270 through 279 removed outlier: 3.609A pdb=" N LEU E 275 " --> pdb=" O TYR E 271 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASP E 276 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN E 277 " --> pdb=" O ASP E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 302 removed outlier: 3.593A pdb=" N LEU E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 320 Processing helix chain 'E' and resid 323 through 343 removed outlier: 5.527A pdb=" N HIS E 329 " --> pdb=" O TYR E 325 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR E 333 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU E 334 " --> pdb=" O GLN E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.744A pdb=" N ILE E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 removed outlier: 3.560A pdb=" N ASP E 364 " --> pdb=" O ALA E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 383 removed outlier: 3.668A pdb=" N PHE E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Proline residue: E 378 - end of helix removed outlier: 3.597A pdb=" N LYS E 382 " --> pdb=" O PRO E 378 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 395 removed outlier: 3.649A pdb=" N VAL E 391 " --> pdb=" O GLU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 424 removed outlier: 4.464A pdb=" N HIS E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 424 " --> pdb=" O HIS E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 436 through 446 removed outlier: 3.651A pdb=" N ILE E 443 " --> pdb=" O LYS E 439 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU E 444 " --> pdb=" O ILE E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 482 removed outlier: 3.509A pdb=" N VAL E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL E 482 " --> pdb=" O PHE E 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 477 through 482' Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 512 through 524 Processing helix chain 'E' and resid 541 through 552 Processing helix chain 'E' and resid 560 through 568 removed outlier: 3.803A pdb=" N LEU E 564 " --> pdb=" O THR E 560 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS E 565 " --> pdb=" O VAL E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 602 removed outlier: 4.004A pdb=" N HIS E 595 " --> pdb=" O LEU E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 609 Processing helix chain 'E' and resid 612 through 624 removed outlier: 4.231A pdb=" N LEU E 616 " --> pdb=" O ASN E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 628 through 636 removed outlier: 3.554A pdb=" N ILE E 632 " --> pdb=" O ASP E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 640 Processing helix chain 'E' and resid 644 through 653 removed outlier: 3.628A pdb=" N GLN E 650 " --> pdb=" O LYS E 646 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG E 653 " --> pdb=" O LYS E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 685 Processing helix chain 'E' and resid 692 through 698 removed outlier: 3.676A pdb=" N HIS E 698 " --> pdb=" O MET E 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 703 through 714 Processing helix chain 'E' and resid 720 through 727 Processing helix chain 'E' and resid 730 through 751 removed outlier: 3.656A pdb=" N LYS E 734 " --> pdb=" O SER E 730 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET E 751 " --> pdb=" O LEU E 747 " (cutoff:3.500A) Processing helix chain 'E' and resid 777 through 792 removed outlier: 3.516A pdb=" N LEU E 791 " --> pdb=" O GLY E 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 802 through 808 Processing helix chain 'E' and resid 808 through 818 Processing helix chain 'E' and resid 861 through 865 removed outlier: 3.547A pdb=" N ARG E 864 " --> pdb=" O ASP E 861 " (cutoff:3.500A) Processing helix chain 'E' and resid 873 through 889 removed outlier: 7.017A pdb=" N ASN E 881 " --> pdb=" O LYS E 877 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR E 882 " --> pdb=" O LYS E 878 " (cutoff:3.500A) Processing helix chain 'E' and resid 893 through 906 removed outlier: 3.775A pdb=" N GLU E 904 " --> pdb=" O LEU E 900 " (cutoff:3.500A) Processing helix chain 'E' and resid 910 through 922 Processing helix chain 'E' and resid 925 through 940 removed outlier: 4.087A pdb=" N LYS E 929 " --> pdb=" O ARG E 925 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN E 940 " --> pdb=" O ASP E 936 " (cutoff:3.500A) Processing helix chain 'E' and resid 960 through 971 removed outlier: 4.089A pdb=" N SER E 964 " --> pdb=" O SER E 960 " (cutoff:3.500A) Processing helix chain 'E' and resid 981 through 1001 removed outlier: 4.002A pdb=" N ALA E 991 " --> pdb=" O ALA E 987 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 992 " --> pdb=" O TYR E 988 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 993 " --> pdb=" O LEU E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 1004 through 1009 Processing helix chain 'E' and resid 1031 through 1041 Processing helix chain 'E' and resid 1078 through 1087 Processing helix chain 'E' and resid 1127 through 1132 Processing helix chain 'E' and resid 1170 through 1177 Processing helix chain 'E' and resid 1177 through 1186 removed outlier: 3.605A pdb=" N PHE E1181 " --> pdb=" O ASN E1177 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS E1185 " --> pdb=" O PHE E1181 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY E1186 " --> pdb=" O LEU E1182 " (cutoff:3.500A) Processing helix chain 'E' and resid 1229 through 1242 removed outlier: 3.730A pdb=" N VAL E1233 " --> pdb=" O PRO E1229 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS E1241 " --> pdb=" O TYR E1237 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR E1242 " --> pdb=" O LEU E1238 " (cutoff:3.500A) Processing helix chain 'E' and resid 1250 through 1262 removed outlier: 3.833A pdb=" N GLN E1254 " --> pdb=" O GLU E1250 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS E1255 " --> pdb=" O ASP E1251 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU E1260 " --> pdb=" O GLN E1256 " (cutoff:3.500A) Processing helix chain 'E' and resid 1265 through 1278 Processing helix chain 'E' and resid 1284 through 1298 removed outlier: 3.618A pdb=" N ARG E1298 " --> pdb=" O TYR E1294 " (cutoff:3.500A) Processing helix chain 'E' and resid 1301 through 1306 Processing helix chain 'E' and resid 1308 through 1313 Processing helix chain 'E' and resid 1340 through 1344 Processing sheet with id=AA1, first strand: chain 'E' and resid 954 through 957 removed outlier: 3.586A pdb=" N VAL E1095 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.725A pdb=" N LEU E 35 " --> pdb=" O ARG E1359 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ASP E1361 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU E1203 " --> pdb=" O ILE E1348 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU E1219 " --> pdb=" O ALA E1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 837 through 840 Processing sheet with id=AA5, first strand: chain 'E' and resid 1063 through 1065 Processing sheet with id=AA6, first strand: chain 'E' and resid 1160 through 1167 removed outlier: 7.018A pdb=" N VAL E1160 " --> pdb=" O VAL E1146 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL E1146 " --> pdb=" O VAL E1160 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU E1162 " --> pdb=" O LEU E1144 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU E1144 " --> pdb=" O GLU E1162 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU E1164 " --> pdb=" O SER E1142 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER E1142 " --> pdb=" O LEU E1164 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE E1166 " --> pdb=" O ALA E1140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 1324 through 1325 removed outlier: 3.574A pdb=" N PHE E1324 " --> pdb=" O ILE E1331 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 210 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 97 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3972 1.34 - 1.46: 4051 1.46 - 1.59: 6125 1.59 - 1.71: 295 1.71 - 1.84: 42 Bond restraints: 14485 Sorted by residual: bond pdb=" C GLY E1319 " pdb=" O GLY E1319 " ideal model delta sigma weight residual 1.236 1.266 -0.030 5.30e-03 3.56e+04 3.25e+01 bond pdb=" CG1 ILE E1050 " pdb=" CD1 ILE E1050 " ideal model delta sigma weight residual 1.513 1.602 -0.089 3.90e-02 6.57e+02 5.16e+00 bond pdb=" CA THR E1051 " pdb=" C THR E1051 " ideal model delta sigma weight residual 1.525 1.566 -0.041 2.10e-02 2.27e+03 3.84e+00 bond pdb=" N THR E1051 " pdb=" CA THR E1051 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.72e+00 bond pdb=" CB GLU E1049 " pdb=" CG GLU E1049 " ideal model delta sigma weight residual 1.520 1.577 -0.057 3.00e-02 1.11e+03 3.60e+00 ... (remaining 14480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 19837 2.05 - 4.09: 311 4.09 - 6.14: 30 6.14 - 8.19: 10 8.19 - 10.23: 2 Bond angle restraints: 20190 Sorted by residual: angle pdb=" N ILE E1050 " pdb=" CA ILE E1050 " pdb=" C ILE E1050 " ideal model delta sigma weight residual 112.96 119.55 -6.59 1.00e+00 1.00e+00 4.34e+01 angle pdb=" C THR E 957 " pdb=" N LEU E 958 " pdb=" CA LEU E 958 " ideal model delta sigma weight residual 121.90 116.74 5.16 1.26e+00 6.30e-01 1.68e+01 angle pdb=" C LEU E 958 " pdb=" CA LEU E 958 " pdb=" CB LEU E 958 " ideal model delta sigma weight residual 112.31 106.60 5.71 1.53e+00 4.27e-01 1.39e+01 angle pdb=" CB MET E 781 " pdb=" CG MET E 781 " pdb=" SD MET E 781 " ideal model delta sigma weight residual 112.70 122.93 -10.23 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C THR E1048 " pdb=" N GLU E1049 " pdb=" CA GLU E1049 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 ... (remaining 20185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 8172 35.42 - 70.84: 595 70.84 - 106.26: 39 106.26 - 141.68: 0 141.68 - 177.10: 3 Dihedral angle restraints: 8809 sinusoidal: 4929 harmonic: 3880 Sorted by residual: dihedral pdb=" CA HIS E1297 " pdb=" C HIS E1297 " pdb=" N ARG E1298 " pdb=" CA ARG E1298 " ideal model delta harmonic sigma weight residual 180.00 153.32 26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA LYS E 356 " pdb=" C LYS E 356 " pdb=" N ASN E 357 " pdb=" CA ASN E 357 " ideal model delta harmonic sigma weight residual 180.00 154.07 25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA TYR E 325 " pdb=" C TYR E 325 " pdb=" N ASP E 326 " pdb=" CA ASP E 326 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 8806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1517 0.031 - 0.062: 547 0.062 - 0.092: 180 0.092 - 0.123: 68 0.123 - 0.154: 16 Chirality restraints: 2328 Sorted by residual: chirality pdb=" CA VAL E 20 " pdb=" N VAL E 20 " pdb=" C VAL E 20 " pdb=" CB VAL E 20 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" P C A 4 " pdb=" OP1 C A 4 " pdb=" OP2 C A 4 " pdb=" O5' C A 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.26 0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" C1' A B 23 " pdb=" O4' A B 23 " pdb=" C2' A B 23 " pdb=" N9 A B 23 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 2325 not shown) Planarity restraints: 2034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E1001 " 0.056 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO E1002 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO E1002 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO E1002 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 502 " 0.044 5.00e-02 4.00e+02 6.77e-02 7.32e+00 pdb=" N PRO E 503 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 503 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 503 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E1242 " -0.015 2.00e-02 2.50e+03 1.75e-02 6.12e+00 pdb=" CG TYR E1242 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR E1242 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E1242 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR E1242 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E1242 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR E1242 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR E1242 " -0.005 2.00e-02 2.50e+03 ... (remaining 2031 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1370 2.74 - 3.28: 12045 3.28 - 3.82: 21628 3.82 - 4.36: 25090 4.36 - 4.90: 41541 Nonbonded interactions: 101674 Sorted by model distance: nonbonded pdb=" N GLU E 438 " pdb=" OE1 GLU E 438 " model vdw 2.205 3.120 nonbonded pdb=" NH1 ARG E 395 " pdb=" OD2 ASP E 397 " model vdw 2.210 3.120 nonbonded pdb=" O SER E1136 " pdb=" OG SER E1136 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASN E1066 " pdb=" OG1 THR E1069 " model vdw 2.254 3.040 nonbonded pdb=" O2' A A 8 " pdb=" OP1 A A 9 " model vdw 2.310 3.040 ... (remaining 101669 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: 5.490 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.430 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 : 0.004 0.089 14485 Z= 0.171 Angle : 0.628 10.233 20190 Z= 0.342 Chirality : 0.039 0.154 2328 Planarity : 0.005 0.085 2034 Dihedral : 20.773 177.095 6293 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.68 % Allowed : 28.81 % Favored : 70.51 % 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 (0.23), residues: 1303 helix: 0.23 (0.22), residues: 604 sheet: 0.18 (0.56), residues: 99 loop : -2.36 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 629 TYR 0.039 0.002 TYR E1242 PHE 0.017 0.001 PHE E 966 TRP 0.009 0.001 TRP E 659 HIS 0.005 0.001 HIS E 983 Details of bonding type rmsd covalent geometry : bond 0.00351 (14485) covalent geometry : angle 0.62812 (20190) hydrogen bonds : bond 0.14079 ( 507) hydrogen bonds : angle 5.06127 ( 1377) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 0.446 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 200 average time/residue: 0.1557 time to fit residues: 42.4947 Evaluate side-chains 198 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 193 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 510 LYS Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain E residue 726 ASN Chi-restraints excluded: chain E residue 1219 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 295 ASN E 668 ASN E 979 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.175783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.129879 restraints weight = 18873.462| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.38 r_work: 0.3101 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14485 Z= 0.164 Angle : 0.582 7.821 20190 Z= 0.312 Chirality : 0.038 0.153 2328 Planarity : 0.004 0.067 2034 Dihedral : 18.783 179.038 3515 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.31 % Allowed : 26.10 % Favored : 70.59 % 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: -1.03 (0.23), residues: 1303 helix: 0.52 (0.22), residues: 617 sheet: 0.45 (0.57), residues: 95 loop : -2.28 (0.22), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 661 TYR 0.011 0.001 TYR E 155 PHE 0.020 0.001 PHE E 966 TRP 0.008 0.001 TRP E 659 HIS 0.006 0.001 HIS E 328 Details of bonding type rmsd covalent geometry : bond 0.00363 (14485) covalent geometry : angle 0.58157 (20190) hydrogen bonds : bond 0.06673 ( 507) hydrogen bonds : angle 4.21422 ( 1377) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: E 274 ASP cc_start: 0.7696 (m-30) cc_final: 0.7465 (m-30) REVERT: E 397 ASP cc_start: 0.7230 (m-30) cc_final: 0.6947 (m-30) REVERT: E 637 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8491 (ttpp) REVERT: E 745 ASP cc_start: 0.7557 (m-30) cc_final: 0.7264 (m-30) REVERT: E 904 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5359 (mp0) REVERT: E 1334 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.7423 (tmtt) outliers start: 39 outliers final: 20 residues processed: 213 average time/residue: 0.1403 time to fit residues: 41.5175 Evaluate side-chains 209 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 512 SER Chi-restraints excluded: chain E residue 578 VAL Chi-restraints excluded: chain E residue 597 LEU Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 657 THR Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 842 VAL Chi-restraints excluded: chain E residue 904 GLU Chi-restraints excluded: chain E residue 929 LYS Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 1072 ILE Chi-restraints excluded: chain E residue 1143 VAL Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1297 HIS Chi-restraints excluded: chain E residue 1327 PHE Chi-restraints excluded: chain E residue 1330 THR Chi-restraints excluded: chain E residue 1334 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 128 optimal weight: 0.0670 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 53 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 979 ASN E 990 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.175286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129320 restraints weight = 18890.557| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.34 r_work: 0.3101 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14485 Z= 0.169 Angle : 0.581 9.037 20190 Z= 0.310 Chirality : 0.039 0.155 2328 Planarity : 0.004 0.063 2034 Dihedral : 18.702 178.798 3505 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.64 % Allowed : 25.51 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.23), residues: 1303 helix: 0.70 (0.22), residues: 611 sheet: 0.58 (0.57), residues: 93 loop : -2.28 (0.22), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 340 TYR 0.012 0.001 TYR E 5 PHE 0.020 0.002 PHE E 966 TRP 0.007 0.001 TRP E 659 HIS 0.005 0.001 HIS E 328 Details of bonding type rmsd covalent geometry : bond 0.00378 (14485) covalent geometry : angle 0.58076 (20190) hydrogen bonds : bond 0.06747 ( 507) hydrogen bonds : angle 4.14019 ( 1377) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: E 274 ASP cc_start: 0.7767 (m-30) cc_final: 0.7486 (m-30) REVERT: E 279 LEU cc_start: 0.8044 (tp) cc_final: 0.7806 (mp) REVERT: E 397 ASP cc_start: 0.7218 (m-30) cc_final: 0.6887 (m-30) REVERT: E 635 ARG cc_start: 0.8345 (tpp80) cc_final: 0.8121 (tpt-90) REVERT: E 745 ASP cc_start: 0.7541 (m-30) cc_final: 0.7195 (m-30) REVERT: E 897 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6689 (p90) REVERT: E 904 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5359 (mp0) REVERT: E 1206 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.6945 (mp) REVERT: E 1347 LEU cc_start: 0.8336 (tp) cc_final: 0.8018 (tp) outliers start: 43 outliers final: 25 residues processed: 217 average time/residue: 0.1434 time to fit residues: 43.2469 Evaluate side-chains 219 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 578 VAL Chi-restraints excluded: chain E residue 597 LEU Chi-restraints excluded: chain E residue 599 LYS Chi-restraints excluded: chain E residue 604 LYS Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 657 THR Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 841 ILE Chi-restraints excluded: chain E residue 842 VAL Chi-restraints excluded: chain E residue 897 PHE Chi-restraints excluded: chain E residue 904 GLU Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain E residue 1065 THR Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1143 VAL Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 1226 LEU Chi-restraints excluded: chain E residue 1297 HIS Chi-restraints excluded: chain E residue 1330 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 125 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 80 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 979 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.174067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.128206 restraints weight = 18725.609| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.38 r_work: 0.3070 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14485 Z= 0.226 Angle : 0.647 9.272 20190 Z= 0.340 Chirality : 0.041 0.226 2328 Planarity : 0.005 0.062 2034 Dihedral : 18.786 178.578 3505 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.07 % Allowed : 24.75 % Favored : 71.19 % 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: -1.00 (0.23), residues: 1303 helix: 0.62 (0.22), residues: 612 sheet: 0.38 (0.55), residues: 95 loop : -2.30 (0.22), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 340 TYR 0.015 0.002 TYR E 5 PHE 0.024 0.002 PHE E 966 TRP 0.007 0.001 TRP E 659 HIS 0.007 0.001 HIS E 328 Details of bonding type rmsd covalent geometry : bond 0.00521 (14485) covalent geometry : angle 0.64671 (20190) hydrogen bonds : bond 0.07949 ( 507) hydrogen bonds : angle 4.23681 ( 1377) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: E 108 GLU cc_start: 0.7373 (tp30) cc_final: 0.7069 (tp30) REVERT: E 397 ASP cc_start: 0.7225 (m-30) cc_final: 0.6868 (m-30) REVERT: E 494 ARG cc_start: 0.8290 (mtp-110) cc_final: 0.7849 (mtm180) REVERT: E 601 ILE cc_start: 0.8191 (tp) cc_final: 0.7908 (tp) REVERT: E 635 ARG cc_start: 0.8332 (tpp80) cc_final: 0.8110 (tpt-90) REVERT: E 637 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8521 (ttpp) REVERT: E 745 ASP cc_start: 0.7559 (m-30) cc_final: 0.7218 (m-30) REVERT: E 897 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6698 (p90) REVERT: E 904 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5382 (mp0) REVERT: E 1005 GLU cc_start: 0.6887 (mp0) cc_final: 0.6669 (mp0) REVERT: E 1166 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8079 (mm) REVERT: E 1206 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6980 (mp) REVERT: E 1334 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.7436 (tmtt) REVERT: E 1347 LEU cc_start: 0.8368 (tp) cc_final: 0.8095 (tp) outliers start: 48 outliers final: 32 residues processed: 218 average time/residue: 0.1328 time to fit residues: 40.0133 Evaluate side-chains 228 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 578 VAL Chi-restraints excluded: chain E residue 597 LEU Chi-restraints excluded: chain E residue 599 LYS Chi-restraints excluded: chain E residue 604 LYS Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain E residue 662 LEU Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 761 ILE Chi-restraints excluded: chain E residue 762 GLU Chi-restraints excluded: chain E residue 822 MET Chi-restraints excluded: chain E residue 841 ILE Chi-restraints excluded: chain E residue 842 VAL Chi-restraints excluded: chain E residue 897 PHE Chi-restraints excluded: chain E residue 904 GLU Chi-restraints excluded: chain E residue 958 LEU Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain E residue 1065 THR Chi-restraints excluded: chain E residue 1085 LYS Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1143 VAL Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1166 ILE Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 1226 LEU Chi-restraints excluded: chain E residue 1297 HIS Chi-restraints excluded: chain E residue 1327 PHE Chi-restraints excluded: chain E residue 1330 THR Chi-restraints excluded: chain E residue 1334 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 54 optimal weight: 2.9990 chunk 77 optimal weight: 50.0000 chunk 126 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 979 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.176991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131126 restraints weight = 18899.818| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.14 r_work: 0.3157 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14485 Z= 0.140 Angle : 0.547 9.435 20190 Z= 0.292 Chirality : 0.038 0.207 2328 Planarity : 0.004 0.055 2034 Dihedral : 18.634 178.623 3502 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.05 % Allowed : 25.85 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.23), residues: 1303 helix: 0.87 (0.22), residues: 610 sheet: 0.63 (0.56), residues: 93 loop : -2.27 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 340 TYR 0.013 0.001 TYR E 325 PHE 0.017 0.001 PHE E 966 TRP 0.006 0.001 TRP E 659 HIS 0.004 0.001 HIS E 412 Details of bonding type rmsd covalent geometry : bond 0.00307 (14485) covalent geometry : angle 0.54736 (20190) hydrogen bonds : bond 0.05734 ( 507) hydrogen bonds : angle 4.00145 ( 1377) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: E 397 ASP cc_start: 0.7389 (m-30) cc_final: 0.6990 (m-30) REVERT: E 635 ARG cc_start: 0.8468 (tpp80) cc_final: 0.8248 (tpt-90) REVERT: E 637 LYS cc_start: 0.8787 (ttmm) cc_final: 0.8581 (ttpp) REVERT: E 661 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7609 (mtt-85) REVERT: E 745 ASP cc_start: 0.7774 (m-30) cc_final: 0.7450 (m-30) REVERT: E 897 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6697 (p90) REVERT: E 904 GLU cc_start: 0.6186 (OUTLIER) cc_final: 0.5355 (mp0) REVERT: E 1005 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6889 (mp0) REVERT: E 1166 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8150 (mm) REVERT: E 1188 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7984 (mttm) REVERT: E 1206 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.6968 (mp) REVERT: E 1334 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.7512 (tmtt) REVERT: E 1347 LEU cc_start: 0.8479 (tp) cc_final: 0.8144 (tt) outliers start: 36 outliers final: 28 residues processed: 209 average time/residue: 0.1357 time to fit residues: 39.4332 Evaluate side-chains 219 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 578 VAL Chi-restraints excluded: chain E residue 597 LEU Chi-restraints excluded: chain E residue 599 LYS Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 762 GLU Chi-restraints excluded: chain E residue 841 ILE Chi-restraints excluded: chain E residue 842 VAL Chi-restraints excluded: chain E residue 897 PHE Chi-restraints excluded: chain E residue 904 GLU Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 958 LEU Chi-restraints excluded: chain E residue 968 LYS Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain E residue 1065 THR Chi-restraints excluded: chain E residue 1085 LYS Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1166 ILE Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 1297 HIS Chi-restraints excluded: chain E residue 1327 PHE Chi-restraints excluded: chain E residue 1330 THR Chi-restraints excluded: chain E residue 1334 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 76 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 0.0370 chunk 118 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 80 optimal weight: 40.0000 chunk 11 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 979 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 = 0.175355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129402 restraints weight = 18646.935| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.19 r_work: 0.3118 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14485 Z= 0.165 Angle : 0.574 10.386 20190 Z= 0.305 Chirality : 0.039 0.181 2328 Planarity : 0.004 0.054 2034 Dihedral : 18.669 178.917 3502 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.73 % Allowed : 25.42 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.23), residues: 1303 helix: 0.88 (0.22), residues: 611 sheet: 0.73 (0.56), residues: 91 loop : -2.29 (0.22), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 340 TYR 0.012 0.001 TYR E 5 PHE 0.019 0.001 PHE E 966 TRP 0.006 0.001 TRP E 659 HIS 0.005 0.001 HIS E 328 Details of bonding type rmsd covalent geometry : bond 0.00368 (14485) covalent geometry : angle 0.57397 (20190) hydrogen bonds : bond 0.06569 ( 507) hydrogen bonds : angle 4.01790 ( 1377) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: E 397 ASP cc_start: 0.7167 (m-30) cc_final: 0.6787 (m-30) REVERT: E 467 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8265 (mtt90) REVERT: E 601 ILE cc_start: 0.8178 (tp) cc_final: 0.7873 (tp) REVERT: E 635 ARG cc_start: 0.8334 (tpp80) cc_final: 0.8103 (tpt-90) REVERT: E 637 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8482 (ttpp) REVERT: E 661 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7444 (mtt-85) REVERT: E 745 ASP cc_start: 0.7497 (m-30) cc_final: 0.7135 (m-30) REVERT: E 897 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6715 (p90) REVERT: E 904 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5383 (mp0) REVERT: E 1005 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6583 (mp0) REVERT: E 1166 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8055 (mm) REVERT: E 1188 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7872 (mttm) REVERT: E 1206 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.6862 (mp) REVERT: E 1334 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.7420 (tmtt) REVERT: E 1347 LEU cc_start: 0.8348 (tp) cc_final: 0.8083 (tt) outliers start: 44 outliers final: 32 residues processed: 214 average time/residue: 0.1359 time to fit residues: 40.4674 Evaluate side-chains 224 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 578 VAL Chi-restraints excluded: chain E residue 597 LEU Chi-restraints excluded: chain E residue 599 LYS Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 662 LEU Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 761 ILE Chi-restraints excluded: chain E residue 762 GLU Chi-restraints excluded: chain E residue 841 ILE Chi-restraints excluded: chain E residue 842 VAL Chi-restraints excluded: chain E residue 897 PHE Chi-restraints excluded: chain E residue 904 GLU Chi-restraints excluded: chain E residue 958 LEU Chi-restraints excluded: chain E residue 968 LYS Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain E residue 1049 GLU Chi-restraints excluded: chain E residue 1065 THR Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1138 THR Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1166 ILE Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 1226 LEU Chi-restraints excluded: chain E residue 1297 HIS Chi-restraints excluded: chain E residue 1327 PHE Chi-restraints excluded: chain E residue 1330 THR Chi-restraints excluded: chain E residue 1334 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 chunk 80 optimal weight: 30.0000 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 40.0000 chunk 69 optimal weight: 0.9990 chunk 88 optimal weight: 50.0000 chunk 35 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 979 ASN E1041 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.175925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128530 restraints weight = 18539.079| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.17 r_work: 0.3126 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14485 Z= 0.156 Angle : 0.562 11.349 20190 Z= 0.299 Chirality : 0.038 0.168 2328 Planarity : 0.004 0.057 2034 Dihedral : 18.639 178.896 3502 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.90 % Allowed : 26.02 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.23), residues: 1303 helix: 0.96 (0.22), residues: 610 sheet: 0.46 (0.55), residues: 95 loop : -2.27 (0.22), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 340 TYR 0.012 0.001 TYR E 325 PHE 0.018 0.001 PHE E 966 TRP 0.005 0.001 TRP E 659 HIS 0.005 0.001 HIS E 328 Details of bonding type rmsd covalent geometry : bond 0.00346 (14485) covalent geometry : angle 0.56216 (20190) hydrogen bonds : bond 0.06081 ( 507) hydrogen bonds : angle 3.96558 ( 1377) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 467 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8249 (mtt90) REVERT: E 524 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7776 (tt) REVERT: E 605 ASP cc_start: 0.8113 (p0) cc_final: 0.7734 (p0) REVERT: E 635 ARG cc_start: 0.8332 (tpp80) cc_final: 0.8103 (tpt-90) REVERT: E 661 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7440 (mtt-85) REVERT: E 745 ASP cc_start: 0.7489 (m-30) cc_final: 0.7141 (m-30) REVERT: E 897 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6735 (p90) REVERT: E 904 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5507 (mp0) REVERT: E 1005 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6578 (mp0) REVERT: E 1166 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8049 (mm) REVERT: E 1188 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7909 (mttm) REVERT: E 1206 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6818 (mp) REVERT: E 1334 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.7417 (tmtt) REVERT: E 1347 LEU cc_start: 0.8354 (tp) cc_final: 0.8077 (tt) outliers start: 46 outliers final: 32 residues processed: 220 average time/residue: 0.1423 time to fit residues: 43.3769 Evaluate side-chains 226 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 578 VAL Chi-restraints excluded: chain E residue 597 LEU Chi-restraints excluded: chain E residue 599 LYS Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 761 ILE Chi-restraints excluded: chain E residue 762 GLU Chi-restraints excluded: chain E residue 841 ILE Chi-restraints excluded: chain E residue 842 VAL Chi-restraints excluded: chain E residue 897 PHE Chi-restraints excluded: chain E residue 904 GLU Chi-restraints excluded: chain E residue 958 LEU Chi-restraints excluded: chain E residue 968 LYS Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain E residue 1049 GLU Chi-restraints excluded: chain E residue 1065 THR Chi-restraints excluded: chain E residue 1085 LYS Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1138 THR Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1166 ILE Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 1226 LEU Chi-restraints excluded: chain E residue 1297 HIS Chi-restraints excluded: chain E residue 1327 PHE Chi-restraints excluded: chain E residue 1330 THR Chi-restraints excluded: chain E residue 1334 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 117 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 979 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.173950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127712 restraints weight = 18532.337| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.28 r_work: 0.3073 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14485 Z= 0.226 Angle : 0.643 11.607 20190 Z= 0.339 Chirality : 0.041 0.178 2328 Planarity : 0.004 0.060 2034 Dihedral : 18.745 178.729 3502 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.41 % Allowed : 25.85 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.23), residues: 1303 helix: 0.78 (0.22), residues: 611 sheet: 0.31 (0.55), residues: 97 loop : -2.33 (0.22), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 340 TYR 0.016 0.002 TYR E 5 PHE 0.023 0.002 PHE E 966 TRP 0.006 0.001 TRP E 659 HIS 0.007 0.001 HIS E 328 Details of bonding type rmsd covalent geometry : bond 0.00520 (14485) covalent geometry : angle 0.64309 (20190) hydrogen bonds : bond 0.07931 ( 507) hydrogen bonds : angle 4.12350 ( 1377) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: E 467 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8764 (mtt90) REVERT: E 524 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7873 (tt) REVERT: E 601 ILE cc_start: 0.8220 (tp) cc_final: 0.7906 (tp) REVERT: E 605 ASP cc_start: 0.8130 (p0) cc_final: 0.7761 (p0) REVERT: E 635 ARG cc_start: 0.8337 (tpp80) cc_final: 0.8110 (tpt-90) REVERT: E 661 ARG cc_start: 0.7755 (ttm-80) cc_final: 0.7474 (mtt-85) REVERT: E 665 LYS cc_start: 0.7442 (tptt) cc_final: 0.6959 (tptt) REVERT: E 745 ASP cc_start: 0.7542 (m-30) cc_final: 0.7191 (m-30) REVERT: E 897 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6739 (p90) REVERT: E 904 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5526 (mp0) REVERT: E 937 SER cc_start: 0.8544 (t) cc_final: 0.8234 (m) REVERT: E 1005 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6631 (mp0) REVERT: E 1166 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8059 (mm) REVERT: E 1170 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7720 (pt0) REVERT: E 1188 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7888 (mttm) REVERT: E 1206 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.6948 (mp) REVERT: E 1334 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.7428 (tmtt) REVERT: E 1347 LEU cc_start: 0.8376 (tp) cc_final: 0.8106 (tt) outliers start: 52 outliers final: 35 residues processed: 222 average time/residue: 0.1453 time to fit residues: 44.4842 Evaluate side-chains 232 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 578 VAL Chi-restraints excluded: chain E residue 597 LEU Chi-restraints excluded: chain E residue 622 THR Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 662 LEU Chi-restraints excluded: chain E residue 743 VAL Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 761 ILE Chi-restraints excluded: chain E residue 762 GLU Chi-restraints excluded: chain E residue 822 MET Chi-restraints excluded: chain E residue 842 VAL Chi-restraints excluded: chain E residue 897 PHE Chi-restraints excluded: chain E residue 904 GLU Chi-restraints excluded: chain E residue 929 LYS Chi-restraints excluded: chain E residue 958 LEU Chi-restraints excluded: chain E residue 968 LYS Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain E residue 1049 GLU Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1138 THR Chi-restraints excluded: chain E residue 1143 VAL Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1166 ILE Chi-restraints excluded: chain E residue 1170 GLU Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 1226 LEU Chi-restraints excluded: chain E residue 1297 HIS Chi-restraints excluded: chain E residue 1327 PHE Chi-restraints excluded: chain E residue 1330 THR Chi-restraints excluded: chain E residue 1334 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 100 optimal weight: 0.0040 chunk 137 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 30.0000 chunk 69 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 979 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.175185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.128934 restraints weight = 18632.145| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.32 r_work: 0.3098 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14485 Z= 0.184 Angle : 0.600 11.697 20190 Z= 0.318 Chirality : 0.040 0.162 2328 Planarity : 0.004 0.062 2034 Dihedral : 18.665 178.427 3502 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.47 % Allowed : 26.69 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.23), residues: 1303 helix: 0.85 (0.22), residues: 611 sheet: 0.31 (0.55), residues: 97 loop : -2.32 (0.22), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 340 TYR 0.014 0.001 TYR E 5 PHE 0.020 0.002 PHE E 966 TRP 0.006 0.001 TRP E 659 HIS 0.006 0.001 HIS E 328 Details of bonding type rmsd covalent geometry : bond 0.00417 (14485) covalent geometry : angle 0.60024 (20190) hydrogen bonds : bond 0.06826 ( 507) hydrogen bonds : angle 4.03416 ( 1377) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 524 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7829 (tt) REVERT: E 601 ILE cc_start: 0.8197 (tp) cc_final: 0.7872 (tp) REVERT: E 605 ASP cc_start: 0.8137 (p0) cc_final: 0.7760 (p0) REVERT: E 635 ARG cc_start: 0.8296 (tpp80) cc_final: 0.8060 (tpt-90) REVERT: E 661 ARG cc_start: 0.7706 (ttm-80) cc_final: 0.7440 (mtt-85) REVERT: E 745 ASP cc_start: 0.7505 (m-30) cc_final: 0.7157 (m-30) REVERT: E 897 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6752 (p90) REVERT: E 904 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5574 (mp0) REVERT: E 1005 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6586 (mp0) REVERT: E 1166 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8072 (mm) REVERT: E 1188 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7884 (mttm) REVERT: E 1206 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6752 (mp) REVERT: E 1334 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.7423 (tmtt) REVERT: E 1347 LEU cc_start: 0.8341 (tp) cc_final: 0.8085 (tt) outliers start: 41 outliers final: 34 residues processed: 215 average time/residue: 0.1302 time to fit residues: 39.1316 Evaluate side-chains 230 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 578 VAL Chi-restraints excluded: chain E residue 597 LEU Chi-restraints excluded: chain E residue 599 LYS Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 743 VAL Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 761 ILE Chi-restraints excluded: chain E residue 762 GLU Chi-restraints excluded: chain E residue 822 MET Chi-restraints excluded: chain E residue 842 VAL Chi-restraints excluded: chain E residue 897 PHE Chi-restraints excluded: chain E residue 904 GLU Chi-restraints excluded: chain E residue 958 LEU Chi-restraints excluded: chain E residue 968 LYS Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain E residue 1049 GLU Chi-restraints excluded: chain E residue 1085 LYS Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1138 THR Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1166 ILE Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 1219 GLU Chi-restraints excluded: chain E residue 1226 LEU Chi-restraints excluded: chain E residue 1297 HIS Chi-restraints excluded: chain E residue 1327 PHE Chi-restraints excluded: chain E residue 1330 THR Chi-restraints excluded: chain E residue 1334 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 940 ASN E 979 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.175417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.129442 restraints weight = 18611.550| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.32 r_work: 0.3103 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14485 Z= 0.167 Angle : 0.588 12.359 20190 Z= 0.312 Chirality : 0.039 0.158 2328 Planarity : 0.004 0.062 2034 Dihedral : 18.652 178.382 3502 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.90 % Allowed : 26.27 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.23), residues: 1303 helix: 0.89 (0.22), residues: 611 sheet: 0.39 (0.55), residues: 95 loop : -2.31 (0.22), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 340 TYR 0.012 0.001 TYR E 5 PHE 0.018 0.001 PHE E 966 TRP 0.005 0.001 TRP E 659 HIS 0.005 0.001 HIS E 328 Details of bonding type rmsd covalent geometry : bond 0.00374 (14485) covalent geometry : angle 0.58779 (20190) hydrogen bonds : bond 0.06564 ( 507) hydrogen bonds : angle 4.02452 ( 1377) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 467 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8671 (mtt90) REVERT: E 524 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7829 (tt) REVERT: E 601 ILE cc_start: 0.8198 (tp) cc_final: 0.7872 (tp) REVERT: E 605 ASP cc_start: 0.8113 (p0) cc_final: 0.7739 (p0) REVERT: E 635 ARG cc_start: 0.8296 (tpp80) cc_final: 0.8058 (tpt-90) REVERT: E 661 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.7436 (mtt-85) REVERT: E 745 ASP cc_start: 0.7483 (m-30) cc_final: 0.7121 (m-30) REVERT: E 897 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6758 (p90) REVERT: E 904 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5587 (mp0) REVERT: E 1005 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6577 (mp0) REVERT: E 1166 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8069 (mm) REVERT: E 1170 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7614 (pt0) REVERT: E 1188 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7885 (mttm) REVERT: E 1206 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6750 (mp) REVERT: E 1334 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.7419 (tmtt) REVERT: E 1347 LEU cc_start: 0.8344 (tp) cc_final: 0.8084 (tt) outliers start: 46 outliers final: 34 residues processed: 219 average time/residue: 0.1395 time to fit residues: 42.2158 Evaluate side-chains 231 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 597 LEU Chi-restraints excluded: chain E residue 599 LYS Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 743 VAL Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 761 ILE Chi-restraints excluded: chain E residue 762 GLU Chi-restraints excluded: chain E residue 822 MET Chi-restraints excluded: chain E residue 842 VAL Chi-restraints excluded: chain E residue 897 PHE Chi-restraints excluded: chain E residue 904 GLU Chi-restraints excluded: chain E residue 940 ASN Chi-restraints excluded: chain E residue 958 LEU Chi-restraints excluded: chain E residue 968 LYS Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain E residue 1049 GLU Chi-restraints excluded: chain E residue 1065 THR Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1138 THR Chi-restraints excluded: chain E residue 1143 VAL Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1166 ILE Chi-restraints excluded: chain E residue 1170 GLU Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 1219 GLU Chi-restraints excluded: chain E residue 1226 LEU Chi-restraints excluded: chain E residue 1297 HIS Chi-restraints excluded: chain E residue 1327 PHE Chi-restraints excluded: chain E residue 1330 THR Chi-restraints excluded: chain E residue 1334 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 81 optimal weight: 50.0000 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 979 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.175283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128922 restraints weight = 18576.782| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.24 r_work: 0.3105 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 14485 Z= 0.212 Angle : 0.806 59.199 20190 Z= 0.465 Chirality : 0.045 0.985 2328 Planarity : 0.004 0.075 2034 Dihedral : 18.659 178.400 3502 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.81 % Allowed : 26.36 % Favored : 69.83 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.23), residues: 1303 helix: 0.89 (0.22), residues: 611 sheet: 0.39 (0.55), residues: 95 loop : -2.31 (0.22), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 340 TYR 0.013 0.001 TYR E 5 PHE 0.018 0.002 PHE E 966 TRP 0.006 0.001 TRP E 659 HIS 0.005 0.001 HIS E 328 Details of bonding type rmsd covalent geometry : bond 0.00453 (14485) covalent geometry : angle 0.80591 (20190) hydrogen bonds : bond 0.06650 ( 507) hydrogen bonds : angle 4.02637 ( 1377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3805.35 seconds wall clock time: 65 minutes 38.12 seconds (3938.12 seconds total)