Starting phenix.real_space_refine on Fri May 16 06:45:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fzt_29639/05_2025/8fzt_29639.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fzt_29639/05_2025/8fzt_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_29639/05_2025/8fzt_29639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fzt_29639/05_2025/8fzt_29639.map" model { file = "/net/cci-nas-00/data/ceres_data/8fzt_29639/05_2025/8fzt_29639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fzt_29639/05_2025/8fzt_29639.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, '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: 9.57, per 1000 atoms: 0.69 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: 3.85 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.74 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: 6.72 Time building geometry restraints manager: 4.50 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 39.200 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.720 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP E 659 HIS 0.005 0.001 HIS E 983 PHE 0.017 0.001 PHE E 966 TYR 0.039 0.002 TYR E1242 ARG 0.018 0.001 ARG E 629 Details of bonding type rmsd hydrogen bonds : bond 0.14079 ( 507) hydrogen bonds : angle 5.06127 ( 1377) covalent geometry : bond 0.00351 (14485) covalent geometry : angle 0.62812 (20190) *********************** 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 : 1.309 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 200 average time/residue: 0.3304 time to fit residues: 90.2189 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 : 1.311 ------------------------------------------------------------------------------- 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 121 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 0.0870 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 84 optimal weight: 40.0000 chunk 130 optimal weight: 0.5980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 E1041 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.176880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130817 restraints weight = 18817.895| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.25 r_work: 0.3132 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14485 Z= 0.141 Angle : 0.555 7.766 20190 Z= 0.298 Chirality : 0.037 0.146 2328 Planarity : 0.004 0.065 2034 Dihedral : 18.750 179.229 3515 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.80 % Allowed : 26.86 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.23), residues: 1303 helix: 0.59 (0.22), residues: 618 sheet: 0.54 (0.57), residues: 96 loop : -2.28 (0.23), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 659 HIS 0.004 0.001 HIS E 328 PHE 0.017 0.001 PHE E 966 TYR 0.012 0.001 TYR E 325 ARG 0.004 0.000 ARG E 221 Details of bonding type rmsd hydrogen bonds : bond 0.06012 ( 507) hydrogen bonds : angle 4.14545 ( 1377) covalent geometry : bond 0.00305 (14485) covalent geometry : angle 0.55465 (20190) *********************** 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 228 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: E 274 ASP cc_start: 0.7685 (m-30) cc_final: 0.7442 (m-30) REVERT: E 397 ASP cc_start: 0.7213 (m-30) cc_final: 0.6930 (m-30) REVERT: E 637 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8466 (ttpp) REVERT: E 745 ASP cc_start: 0.7519 (m-30) cc_final: 0.7218 (m-30) REVERT: E 904 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5347 (mp0) REVERT: E 1347 LEU cc_start: 0.8355 (tp) cc_final: 0.8087 (tt) outliers start: 33 outliers final: 15 residues processed: 213 average time/residue: 0.3281 time to fit residues: 98.1388 Evaluate side-chains 205 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 512 SER 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 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 1188 LYS Chi-restraints excluded: chain E residue 1327 PHE Chi-restraints excluded: chain E residue 1330 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 32 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 40 optimal weight: 0.3980 chunk 119 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 84 optimal weight: 50.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.172816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126366 restraints weight = 18725.339| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.36 r_work: 0.3049 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14485 Z= 0.272 Angle : 0.706 9.555 20190 Z= 0.371 Chirality : 0.044 0.197 2328 Planarity : 0.005 0.068 2034 Dihedral : 18.903 178.321 3505 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.07 % Allowed : 25.76 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.23), residues: 1303 helix: 0.40 (0.22), residues: 617 sheet: 0.31 (0.56), residues: 95 loop : -2.37 (0.22), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 659 HIS 0.009 0.002 HIS E 328 PHE 0.028 0.002 PHE E 966 TYR 0.017 0.002 TYR E1141 ARG 0.008 0.001 ARG E 340 Details of bonding type rmsd hydrogen bonds : bond 0.09265 ( 507) hydrogen bonds : angle 4.41737 ( 1377) covalent geometry : bond 0.00631 (14485) covalent geometry : angle 0.70588 (20190) *********************** 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 244 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 1.447 Fit side-chains revert: symmetry clash REVERT: E 279 LEU cc_start: 0.8105 (tp) cc_final: 0.7883 (mp) REVERT: E 397 ASP cc_start: 0.7233 (m-30) cc_final: 0.6902 (m-30) REVERT: E 745 ASP cc_start: 0.7571 (m-30) cc_final: 0.7265 (m-30) REVERT: E 897 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.6701 (p90) REVERT: E 904 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5375 (mp0) REVERT: E 1166 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8090 (mm) REVERT: E 1206 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7047 (mp) REVERT: E 1334 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.7454 (tmtt) outliers start: 48 outliers final: 24 residues processed: 225 average time/residue: 0.3060 time to fit residues: 95.9645 Evaluate side-chains 221 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 376 ILE Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 483 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 604 LYS Chi-restraints excluded: chain E residue 622 THR Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 662 LEU Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 761 ILE 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 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 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 Chi-restraints excluded: chain E residue 1334 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.175829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130179 restraints weight = 18866.901| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.30 r_work: 0.3120 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1313 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= 0.148 Angle : 0.561 8.784 20190 Z= 0.299 Chirality : 0.038 0.185 2328 Planarity : 0.004 0.058 2034 Dihedral : 18.714 178.534 3505 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.71 % Allowed : 26.27 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.23), residues: 1303 helix: 0.74 (0.22), residues: 610 sheet: 0.63 (0.56), residues: 92 loop : -2.30 (0.22), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 659 HIS 0.005 0.001 HIS E 412 PHE 0.017 0.001 PHE E 966 TYR 0.014 0.001 TYR E 325 ARG 0.005 0.000 ARG E 340 Details of bonding type rmsd hydrogen bonds : bond 0.05946 ( 507) hydrogen bonds : angle 4.09373 ( 1377) covalent geometry : bond 0.00322 (14485) covalent geometry : angle 0.56073 (20190) *********************** 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 225 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: E 397 ASP cc_start: 0.7207 (m-30) cc_final: 0.6849 (m-30) REVERT: E 601 ILE cc_start: 0.8166 (tp) cc_final: 0.7876 (tp) REVERT: E 637 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8497 (ttpp) REVERT: E 745 ASP cc_start: 0.7510 (m-30) cc_final: 0.7162 (m-30) REVERT: E 897 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6694 (p90) REVERT: E 904 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5377 (mp0) REVERT: E 1206 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6866 (mp) REVERT: E 1334 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.7429 (tmtt) REVERT: E 1347 LEU cc_start: 0.8353 (tp) cc_final: 0.8051 (tp) outliers start: 32 outliers final: 22 residues processed: 211 average time/residue: 0.3025 time to fit residues: 88.8542 Evaluate side-chains 218 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 483 ASP 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 650 GLN Chi-restraints excluded: chain E residue 657 THR Chi-restraints excluded: chain E residue 706 GLU 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 968 LYS Chi-restraints excluded: chain E residue 1065 THR Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 1219 GLU 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 130 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 21 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.176584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130255 restraints weight = 18757.338| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.09 r_work: 0.3144 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1471 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= 0.138 Angle : 0.546 9.493 20190 Z= 0.291 Chirality : 0.037 0.154 2328 Planarity : 0.004 0.061 2034 Dihedral : 18.674 178.835 3505 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.97 % Allowed : 26.02 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.23), residues: 1303 helix: 0.92 (0.22), residues: 610 sheet: 0.66 (0.56), residues: 92 loop : -2.27 (0.22), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 659 HIS 0.004 0.001 HIS E 412 PHE 0.016 0.001 PHE E 966 TYR 0.013 0.001 TYR E 325 ARG 0.006 0.000 ARG E 340 Details of bonding type rmsd hydrogen bonds : bond 0.05768 ( 507) hydrogen bonds : angle 3.98778 ( 1377) covalent geometry : bond 0.00301 (14485) covalent geometry : angle 0.54572 (20190) *********************** 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: 35 poor density : 190 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: E 495 MET cc_start: 0.8450 (ptm) cc_final: 0.8248 (ptt) REVERT: E 637 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8471 (ttpp) REVERT: E 661 ARG cc_start: 0.7770 (ttm-80) cc_final: 0.7429 (mtt-85) REVERT: E 745 ASP cc_start: 0.7490 (m-30) cc_final: 0.7140 (m-30) REVERT: E 897 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6687 (p90) REVERT: E 904 GLU cc_start: 0.6188 (OUTLIER) cc_final: 0.5349 (mp0) REVERT: E 1206 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6806 (mp) REVERT: E 1334 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.7406 (tmtt) REVERT: E 1347 LEU cc_start: 0.8342 (tp) cc_final: 0.8074 (tt) outliers start: 35 outliers final: 28 residues processed: 211 average time/residue: 0.3455 time to fit residues: 99.8982 Evaluate side-chains 224 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 282 ILE 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 650 GLN Chi-restraints excluded: chain E residue 657 THR Chi-restraints excluded: chain E residue 761 ILE 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 937 SER Chi-restraints excluded: chain E residue 958 LEU Chi-restraints excluded: chain E residue 968 LYS 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 1206 LEU Chi-restraints excluded: chain E residue 1219 GLU 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 31 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 40.0000 chunk 143 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 81 optimal weight: 40.0000 chunk 76 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.174626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128625 restraints weight = 18819.909| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.36 r_work: 0.3084 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1587 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= 0.197 Angle : 0.607 10.280 20190 Z= 0.322 Chirality : 0.040 0.166 2328 Planarity : 0.004 0.056 2034 Dihedral : 18.715 178.915 3502 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.90 % Allowed : 25.68 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.23), residues: 1303 helix: 0.83 (0.22), residues: 611 sheet: 0.44 (0.56), residues: 95 loop : -2.29 (0.22), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 659 HIS 0.007 0.001 HIS E 328 PHE 0.021 0.002 PHE E 966 TYR 0.013 0.001 TYR E 5 ARG 0.007 0.000 ARG E 340 Details of bonding type rmsd hydrogen bonds : bond 0.07315 ( 507) hydrogen bonds : angle 4.10248 ( 1377) covalent geometry : bond 0.00446 (14485) covalent geometry : angle 0.60708 (20190) *********************** 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 242 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 1.433 Fit side-chains revert: symmetry clash REVERT: E 395 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.6260 (ttp-170) REVERT: E 397 ASP cc_start: 0.7205 (m-30) cc_final: 0.6841 (m-30) REVERT: E 467 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8456 (mtt90) REVERT: E 601 ILE cc_start: 0.8185 (tp) cc_final: 0.7884 (tp) REVERT: E 637 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8513 (ttpp) REVERT: E 661 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7434 (mtt-85) REVERT: E 745 ASP cc_start: 0.7556 (m-30) cc_final: 0.7199 (m-30) REVERT: E 897 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.6733 (p90) REVERT: E 904 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5426 (mp0) REVERT: E 1166 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8041 (mm) REVERT: E 1206 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.6878 (mp) REVERT: E 1268 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: E 1334 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.7433 (tmtt) REVERT: E 1347 LEU cc_start: 0.8362 (tp) cc_final: 0.8091 (tt) outliers start: 46 outliers final: 32 residues processed: 225 average time/residue: 0.3142 time to fit residues: 98.5179 Evaluate side-chains 232 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 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 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 650 GLN 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 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 1206 LEU Chi-restraints excluded: chain E residue 1219 GLU Chi-restraints excluded: chain E residue 1226 LEU Chi-restraints excluded: chain E residue 1268 GLU 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 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 100 optimal weight: 0.0370 chunk 39 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.177175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.130538 restraints weight = 18743.176| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.09 r_work: 0.3152 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1718 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= 0.126 Angle : 0.530 11.060 20190 Z= 0.283 Chirality : 0.037 0.147 2328 Planarity : 0.004 0.056 2034 Dihedral : 18.634 178.782 3502 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.97 % Allowed : 27.12 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1303 helix: 1.04 (0.22), residues: 610 sheet: 0.58 (0.55), residues: 96 loop : -2.28 (0.22), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 659 HIS 0.004 0.001 HIS E 328 PHE 0.015 0.001 PHE E 966 TYR 0.015 0.001 TYR E 325 ARG 0.005 0.000 ARG E 340 Details of bonding type rmsd hydrogen bonds : bond 0.05308 ( 507) hydrogen bonds : angle 3.91351 ( 1377) covalent geometry : bond 0.00272 (14485) covalent geometry : angle 0.53046 (20190) *********************** 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 231 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 397 ASP cc_start: 0.7166 (m-30) cc_final: 0.6763 (m-30) REVERT: E 467 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8278 (mtt90) REVERT: E 524 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7746 (tt) REVERT: E 605 ASP cc_start: 0.8118 (p0) cc_final: 0.7745 (p0) REVERT: E 661 ARG cc_start: 0.7727 (ttm-80) cc_final: 0.7428 (mtt-85) REVERT: E 745 ASP cc_start: 0.7483 (m-30) cc_final: 0.7127 (m-30) REVERT: E 897 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6738 (p90) REVERT: E 904 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5450 (mp0) REVERT: E 1206 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6787 (mp) REVERT: E 1334 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.7409 (tmtt) REVERT: E 1347 LEU cc_start: 0.8335 (tp) cc_final: 0.8078 (tt) outliers start: 35 outliers final: 24 residues processed: 220 average time/residue: 0.3054 time to fit residues: 93.4336 Evaluate side-chains 223 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 958 LEU Chi-restraints excluded: chain E residue 968 LYS 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 1146 VAL Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 1219 GLU 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 100 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 940 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.174202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.128203 restraints weight = 18589.194| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.24 r_work: 0.3092 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14485 Z= 0.205 Angle : 0.616 11.670 20190 Z= 0.326 Chirality : 0.040 0.171 2328 Planarity : 0.004 0.060 2034 Dihedral : 18.719 178.859 3502 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.81 % Allowed : 26.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.23), residues: 1303 helix: 0.81 (0.22), residues: 617 sheet: 0.35 (0.55), residues: 97 loop : -2.32 (0.22), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 659 HIS 0.007 0.001 HIS E 328 PHE 0.021 0.002 PHE E 966 TYR 0.013 0.002 TYR E 5 ARG 0.007 0.000 ARG E 340 Details of bonding type rmsd hydrogen bonds : bond 0.07491 ( 507) hydrogen bonds : angle 4.08950 ( 1377) covalent geometry : bond 0.00469 (14485) covalent geometry : angle 0.61627 (20190) *********************** 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 245 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 467 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8708 (mtt90) REVERT: E 524 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7843 (tt) REVERT: E 601 ILE cc_start: 0.8220 (tp) cc_final: 0.7908 (tp) REVERT: E 605 ASP cc_start: 0.8105 (p0) cc_final: 0.7731 (p0) REVERT: E 661 ARG cc_start: 0.7741 (ttm-80) cc_final: 0.7459 (mtt-85) REVERT: E 745 ASP cc_start: 0.7555 (m-30) cc_final: 0.7209 (m-30) REVERT: E 897 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6746 (p90) REVERT: E 904 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5513 (mp0) REVERT: E 1166 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8045 (mm) REVERT: E 1170 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7728 (pt0) REVERT: E 1206 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6840 (mp) REVERT: E 1268 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: E 1334 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.7421 (tmtt) REVERT: E 1347 LEU cc_start: 0.8362 (tp) cc_final: 0.8099 (tt) outliers start: 45 outliers final: 34 residues processed: 232 average time/residue: 0.3039 time to fit residues: 97.9039 Evaluate side-chains 239 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 650 GLN 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 940 ASN Chi-restraints excluded: chain E residue 958 LEU Chi-restraints excluded: chain E residue 968 LYS 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 1170 GLU 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 1268 GLU 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 11 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 87 optimal weight: 40.0000 chunk 122 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 127 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.177615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132413 restraints weight = 18557.738| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.37 r_work: 0.3150 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14485 Z= 0.116 Angle : 0.524 12.491 20190 Z= 0.280 Chirality : 0.036 0.147 2328 Planarity : 0.004 0.059 2034 Dihedral : 18.596 178.658 3502 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.88 % Allowed : 27.46 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.23), residues: 1303 helix: 1.05 (0.22), residues: 617 sheet: 0.52 (0.55), residues: 96 loop : -2.29 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 659 HIS 0.004 0.001 HIS E 412 PHE 0.012 0.001 PHE E 966 TYR 0.016 0.001 TYR E 325 ARG 0.005 0.000 ARG E 340 Details of bonding type rmsd hydrogen bonds : bond 0.04827 ( 507) hydrogen bonds : angle 3.87451 ( 1377) covalent geometry : bond 0.00242 (14485) covalent geometry : angle 0.52389 (20190) *********************** 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 225 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 467 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8266 (mtt90) REVERT: E 524 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7793 (tt) REVERT: E 605 ASP cc_start: 0.8103 (p0) cc_final: 0.7738 (p0) REVERT: E 661 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.7432 (mtt-85) REVERT: E 665 LYS cc_start: 0.7459 (tptt) cc_final: 0.7034 (tptt) REVERT: E 745 ASP cc_start: 0.7475 (m-30) cc_final: 0.7120 (m-30) REVERT: E 897 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6704 (p90) REVERT: E 904 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5521 (mp0) REVERT: E 939 MET cc_start: 0.8049 (tpp) cc_final: 0.7642 (tpp) REVERT: E 1206 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6739 (mp) REVERT: E 1334 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.7416 (tmtt) REVERT: E 1347 LEU cc_start: 0.8342 (tp) cc_final: 0.8082 (tt) outliers start: 34 outliers final: 24 residues processed: 214 average time/residue: 0.3101 time to fit residues: 91.3598 Evaluate side-chains 222 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 395 ARG 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 642 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 743 VAL 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 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 1206 LEU Chi-restraints excluded: chain E residue 1219 GLU 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 64 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.176223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.130012 restraints weight = 18646.340| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.35 r_work: 0.3114 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1936 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 12.648 20190 Z= 0.299 Chirality : 0.038 0.151 2328 Planarity : 0.004 0.057 2034 Dihedral : 18.620 178.796 3502 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.80 % Allowed : 27.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.23), residues: 1303 helix: 1.06 (0.22), residues: 616 sheet: 0.50 (0.55), residues: 95 loop : -2.28 (0.22), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 659 HIS 0.005 0.001 HIS E 328 PHE 0.017 0.001 PHE E 966 TYR 0.011 0.001 TYR E 325 ARG 0.006 0.000 ARG E 340 Details of bonding type rmsd hydrogen bonds : bond 0.06165 ( 507) hydrogen bonds : angle 3.93283 ( 1377) covalent geometry : bond 0.00347 (14485) covalent geometry : angle 0.56195 (20190) ********************** 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 228 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: E 467 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8346 (mtt90) REVERT: E 524 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7798 (tt) REVERT: E 605 ASP cc_start: 0.8131 (p0) cc_final: 0.7761 (p0) REVERT: E 661 ARG cc_start: 0.7681 (ttm-80) cc_final: 0.7443 (mtt-85) REVERT: E 665 LYS cc_start: 0.7483 (tptt) cc_final: 0.7040 (tptt) REVERT: E 745 ASP cc_start: 0.7525 (m-30) cc_final: 0.7166 (m-30) REVERT: E 897 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6740 (p90) REVERT: E 904 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5571 (mp0) REVERT: E 1206 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6754 (mp) REVERT: E 1334 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.7412 (tmtt) REVERT: E 1347 LEU cc_start: 0.8352 (tp) cc_final: 0.8095 (tt) outliers start: 33 outliers final: 25 residues processed: 218 average time/residue: 0.3198 time to fit residues: 96.3735 Evaluate side-chains 225 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN 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 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 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 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 1206 LEU Chi-restraints excluded: chain E residue 1219 GLU 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 95 optimal weight: 0.0270 chunk 16 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.177790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.132168 restraints weight = 18675.555| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.37 r_work: 0.3149 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2017 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= 0.123 Angle : 0.532 12.638 20190 Z= 0.283 Chirality : 0.036 0.146 2328 Planarity : 0.004 0.056 2034 Dihedral : 18.575 178.682 3502 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.80 % Allowed : 27.20 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.23), residues: 1303 helix: 1.17 (0.22), residues: 611 sheet: 0.53 (0.54), residues: 96 loop : -2.22 (0.22), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 659 HIS 0.004 0.001 HIS E 412 PHE 0.014 0.001 PHE E 966 TYR 0.015 0.001 TYR E 325 ARG 0.007 0.000 ARG E 340 Details of bonding type rmsd hydrogen bonds : bond 0.05101 ( 507) hydrogen bonds : angle 3.84868 ( 1377) covalent geometry : bond 0.00266 (14485) covalent geometry : angle 0.53246 (20190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7478.29 seconds wall clock time: 130 minutes 24.57 seconds (7824.57 seconds total)