Starting phenix.real_space_refine on Thu Aug 6 07:09:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fzt_29639/08_2026/8fzt_29639.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fzt_29639/08_2026/8fzt_29639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8fzt_29639/08_2026/8fzt_29639.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fzt_29639/08_2026/8fzt_29639.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fzt_29639/08_2026/8fzt_29639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fzt_29639/08_2026/8fzt_29639.map" model { file = "/net/cci-nas-00/data/ceres_data/8fzt_29639/08_2026/8fzt_29639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fzt_29639/08_2026/8fzt_29639.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 149 5.49 5 S 22 5.16 5 C 8303 2.51 5 N 2436 2.21 5 O 3015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "E GLU 706": not complete - not flipped Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13925 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 10780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10780 Classifications: {'peptide': 1319} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 35, 'TRANS': 1283} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 803 Classifications: {'RNAv2': 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: {'RNAv2': 69} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 24} Link IDs: {'rna2p': 11, 'rna3p': 57} Chain: "C" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 616 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 2.16, per 1000 atoms: 0.16 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: 0.77 Conformation dependent library (CDL) restraints added in 547.1 milliseconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2516 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 7 sheets defined 50.6% alpha, 6.0% beta 42 base pairs and 97 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'E' and resid 59 through 87 removed outlier: 4.112A pdb=" N ARG E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE E 79 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS E 80 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR E 81 " --> pdb=" O ASN E 77 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU E 82 " --> pdb=" O ARG E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.562A pdb=" N VAL E 93 " --> pdb=" O MET E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.578A pdb=" N ARG E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 101 " --> pdb=" O PHE E 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 96 through 101' Processing helix chain 'E' and resid 122 through 132 removed outlier: 3.922A pdb=" N VAL E 126 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA E 127 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N TYR E 128 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 145 removed outlier: 4.213A pdb=" N LEU E 138 " --> pdb=" O THR E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 164 removed outlier: 3.779A pdb=" N ILE E 154 " --> pdb=" O ASP E 150 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE E 164 " --> pdb=" O HIS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 196 Processing helix chain 'E' and resid 207 through 213 removed outlier: 3.668A pdb=" N ILE E 211 " --> pdb=" O ASP E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 229 removed outlier: 3.703A pdb=" N GLN E 228 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU E 229 " --> pdb=" O LEU E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 247 Processing helix chain 'E' and resid 253 through 257 removed outlier: 3.650A pdb=" N PHE E 256 " --> pdb=" O LYS E 253 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP E 257 " --> pdb=" O SER E 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 253 through 257' Processing helix chain 'E' and resid 270 through 279 removed outlier: 3.609A pdb=" N LEU E 275 " --> pdb=" O TYR E 271 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASP E 276 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN E 277 " --> pdb=" O ASP E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 302 removed outlier: 3.593A pdb=" N LEU E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 320 Processing helix chain 'E' and resid 323 through 343 removed outlier: 5.527A pdb=" N HIS E 329 " --> pdb=" O TYR E 325 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR E 333 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU E 334 " --> pdb=" O GLN E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.744A pdb=" N ILE E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 removed outlier: 3.560A pdb=" N ASP E 364 " --> pdb=" O ALA E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 383 removed outlier: 3.668A pdb=" N PHE E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Proline residue: E 378 - end of helix removed outlier: 3.597A pdb=" N LYS E 382 " --> pdb=" O PRO E 378 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 395 removed outlier: 3.649A pdb=" N VAL E 391 " --> pdb=" O GLU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 424 removed outlier: 4.464A pdb=" N HIS E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 424 " --> pdb=" O HIS E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 436 through 446 removed outlier: 3.651A pdb=" N ILE E 443 " --> pdb=" O LYS E 439 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU E 444 " --> pdb=" O ILE E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 482 removed outlier: 3.509A pdb=" N VAL E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL E 482 " --> pdb=" O PHE E 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 477 through 482' Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 512 through 524 Processing helix chain 'E' and resid 541 through 552 Processing helix chain 'E' and resid 560 through 568 removed outlier: 3.803A pdb=" N LEU E 564 " --> pdb=" O THR E 560 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS E 565 " --> pdb=" O VAL E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 602 removed outlier: 4.004A pdb=" N HIS E 595 " --> pdb=" O LEU E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 609 Processing helix chain 'E' and resid 612 through 624 removed outlier: 4.231A pdb=" N LEU E 616 " --> pdb=" O ASN E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 628 through 636 removed outlier: 3.554A pdb=" N ILE E 632 " --> pdb=" O ASP E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 640 Processing helix chain 'E' and resid 644 through 653 removed outlier: 3.628A pdb=" N GLN E 650 " --> pdb=" O LYS E 646 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG E 653 " --> pdb=" O LYS E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 685 Processing helix chain 'E' and resid 692 through 698 removed outlier: 3.676A pdb=" N HIS E 698 " --> pdb=" O MET E 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 703 through 714 Processing helix chain 'E' and resid 720 through 727 Processing helix chain 'E' and resid 730 through 751 removed outlier: 3.656A pdb=" N LYS E 734 " --> pdb=" O SER E 730 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET E 751 " --> pdb=" O LEU E 747 " (cutoff:3.500A) Processing helix chain 'E' and resid 777 through 792 removed outlier: 3.516A pdb=" N LEU E 791 " --> pdb=" O GLY E 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 802 through 808 Processing helix chain 'E' and resid 808 through 818 Processing helix chain 'E' and resid 861 through 865 removed outlier: 3.547A pdb=" N ARG E 864 " --> pdb=" O ASP E 861 " (cutoff:3.500A) Processing helix chain 'E' and resid 873 through 889 removed outlier: 7.017A pdb=" N ASN E 881 " --> pdb=" O LYS E 877 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR E 882 " --> pdb=" O LYS E 878 " (cutoff:3.500A) Processing helix chain 'E' and resid 893 through 906 removed outlier: 3.775A pdb=" N GLU E 904 " --> pdb=" O LEU E 900 " (cutoff:3.500A) Processing helix chain 'E' and resid 910 through 922 Processing helix chain 'E' and resid 925 through 940 removed outlier: 4.087A pdb=" N LYS E 929 " --> pdb=" O ARG E 925 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN E 940 " --> pdb=" O ASP E 936 " (cutoff:3.500A) Processing helix chain 'E' and resid 960 through 971 removed outlier: 4.089A pdb=" N SER E 964 " --> pdb=" O SER E 960 " (cutoff:3.500A) Processing helix chain 'E' and resid 981 through 1001 removed outlier: 4.002A pdb=" N ALA E 991 " --> pdb=" O ALA E 987 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 992 " --> pdb=" O TYR E 988 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 993 " --> pdb=" O LEU E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 1004 through 1009 Processing helix chain 'E' and resid 1031 through 1041 Processing helix chain 'E' and resid 1078 through 1087 Processing helix chain 'E' and resid 1127 through 1132 Processing helix chain 'E' and resid 1170 through 1177 Processing helix chain 'E' and resid 1177 through 1186 removed outlier: 3.605A pdb=" N PHE E1181 " --> pdb=" O ASN E1177 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS E1185 " --> pdb=" O PHE E1181 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY E1186 " --> pdb=" O LEU E1182 " (cutoff:3.500A) Processing helix chain 'E' and resid 1229 through 1242 removed outlier: 3.730A pdb=" N VAL E1233 " --> pdb=" O PRO E1229 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS E1241 " --> pdb=" O TYR E1237 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR E1242 " --> pdb=" O LEU E1238 " (cutoff:3.500A) Processing helix chain 'E' and resid 1250 through 1262 removed outlier: 3.833A pdb=" N GLN E1254 " --> pdb=" O GLU E1250 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS E1255 " --> pdb=" O ASP E1251 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU E1260 " --> pdb=" O GLN E1256 " (cutoff:3.500A) Processing helix chain 'E' and resid 1265 through 1278 Processing helix chain 'E' and resid 1284 through 1298 removed outlier: 3.618A pdb=" N ARG E1298 " --> pdb=" O TYR E1294 " (cutoff:3.500A) Processing helix chain 'E' and resid 1301 through 1306 Processing helix chain 'E' and resid 1308 through 1313 Processing helix chain 'E' and resid 1340 through 1344 Processing sheet with id=AA1, first strand: chain 'E' and resid 954 through 957 removed outlier: 3.586A pdb=" N VAL E1095 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.725A pdb=" N LEU E 35 " --> pdb=" O ARG E1359 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ASP E1361 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU E1203 " --> pdb=" O ILE E1348 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU E1219 " --> pdb=" O ALA E1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 837 through 840 Processing sheet with id=AA5, first strand: chain 'E' and resid 1063 through 1065 Processing sheet with id=AA6, first strand: chain 'E' and resid 1160 through 1167 removed outlier: 7.018A pdb=" N VAL E1160 " --> pdb=" O VAL E1146 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL E1146 " --> pdb=" O VAL E1160 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU E1162 " --> pdb=" O LEU E1144 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU E1144 " --> pdb=" O GLU E1162 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU E1164 " --> pdb=" O SER E1142 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER E1142 " --> pdb=" O LEU E1164 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE E1166 " --> pdb=" O ALA E1140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 1324 through 1325 removed outlier: 3.574A pdb=" N PHE E1324 " --> pdb=" O ILE E1331 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 210 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 97 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 1.12 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=" C3' DT D 28 " pdb=" C2' DT D 28 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT C 21 " pdb=" C2' DT C 21 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.25e+00 bond pdb=" C3' DG C 22 " pdb=" C2' DG C 22 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.15e+00 bond pdb=" C3' DT D 27 " pdb=" C2' DT D 27 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.45e+00 ... (remaining 14480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 19526 2.05 - 4.09: 598 4.09 - 6.14: 54 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=" O4' DG C 13 " pdb=" C4' DG C 13 " pdb=" C3' DG C 13 " ideal model delta sigma weight residual 106.00 102.88 3.12 6.00e-01 2.78e+00 2.71e+01 angle pdb=" O4' DG C 15 " pdb=" C4' DG C 15 " pdb=" C3' DG C 15 " ideal model delta sigma weight residual 106.00 102.89 3.11 6.00e-01 2.78e+00 2.69e+01 angle pdb=" O4' DG C 12 " pdb=" C4' DG C 12 " pdb=" C3' DG C 12 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.46e+01 angle pdb=" N3 DT D 27 " pdb=" C4 DT D 27 " pdb=" O4 DT D 27 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 ... (remaining 20185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 7851 35.42 - 70.84: 596 70.84 - 106.26: 25 106.26 - 141.68: 0 141.68 - 177.10: 3 Dihedral angle restraints: 8475 sinusoidal: 4595 harmonic: 3880 Sorted by residual: dihedral pdb=" C4' U B 35 " pdb=" C3' U B 35 " pdb=" C2' U B 35 " pdb=" C1' U B 35 " ideal model delta sinusoidal sigma weight residual 36.34 -36.54 72.89 1 3.10e+00 1.04e-01 7.05e+02 dihedral pdb=" C4' C B 27 " pdb=" C3' C B 27 " pdb=" C2' C B 27 " pdb=" C1' C B 27 " ideal model delta sinusoidal sigma weight residual 36.34 -36.11 72.46 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" C4' G B 61 " pdb=" C3' G B 61 " pdb=" C2' G B 61 " pdb=" C1' G B 61 " ideal model delta sinusoidal sigma weight residual 36.35 -35.91 72.25 1 3.10e+00 1.04e-01 6.94e+02 ... (remaining 8472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1853 0.057 - 0.115: 311 0.115 - 0.172: 33 0.172 - 0.230: 41 0.230 - 0.287: 90 Chirality restraints: 2328 Sorted by residual: chirality pdb=" C2' C B 27 " pdb=" C3' C B 27 " pdb=" O2' C B 27 " pdb=" C1' C B 27 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" P C B 32 " pdb=" OP1 C B 32 " pdb=" OP2 C B 32 " pdb=" O5' C B 32 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C2' A B 29 " pdb=" C3' A B 29 " pdb=" O2' A B 29 " pdb=" C1' A B 29 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (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: 4.750 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.950 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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= 0.264 Angle : 0.751 10.233 20190 Z= 0.441 Chirality : 0.070 0.287 2328 Planarity : 0.005 0.085 2034 Dihedral : 20.617 177.095 5959 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.68 % Allowed : 28.81 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.23), residues: 1303 helix: 0.23 (0.22), residues: 604 sheet: 0.18 (0.56), residues: 99 loop : -2.36 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 629 TYR 0.039 0.002 TYR E1242 PHE 0.017 0.001 PHE E 966 TRP 0.009 0.001 TRP E 659 HIS 0.005 0.001 HIS E 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.26 (14485) covalent geometry : angle 0.75109 / 0.44 (20190) hydrogen bonds : bond 0.14079 / 9.35 ( 507) hydrogen bonds : angle 5.06127 / 3.37 ( 1377) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 0.427 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 200 average time/residue: 0.1299 time to fit residues: 35.8769 Evaluate side-chains 198 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 193 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 510 LYS Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain E residue 726 ASN Chi-restraints excluded: chain E residue 1219 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 668 ASN E 979 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.176885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130532 restraints weight = 18855.147| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.33 r_work: 0.3127 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14485 Z= 0.189 Angle : 0.937 20.503 20190 Z= 0.425 Chirality : 0.088 1.225 2328 Planarity : 0.004 0.066 2034 Dihedral : 17.038 179.355 3181 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.88 % Allowed : 25.93 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.23), residues: 1303 helix: 0.49 (0.22), residues: 616 sheet: 0.50 (0.57), residues: 95 loop : -2.25 (0.23), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 661 TYR 0.012 0.001 TYR E 362 PHE 0.017 0.001 PHE E 966 TRP 0.008 0.001 TRP E 659 HIS 0.005 0.001 HIS E 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (14485) covalent geometry : angle 0.93701 / 0.42 (20190) hydrogen bonds : bond 0.06909 / 4.59 ( 507) hydrogen bonds : angle 4.31805 / 2.98 ( 1377) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: E 397 ASP cc_start: 0.7273 (m-30) cc_final: 0.6994 (m-30) REVERT: E 745 ASP cc_start: 0.7597 (m-30) cc_final: 0.7347 (m-30) REVERT: E 1188 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7879 (mttm) REVERT: E 1206 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.6890 (mp) outliers start: 34 outliers final: 13 residues processed: 210 average time/residue: 0.1277 time to fit residues: 37.4944 Evaluate side-chains 204 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 578 VAL Chi-restraints excluded: chain E residue 597 LEU Chi-restraints excluded: chain E residue 657 THR Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 842 VAL Chi-restraints excluded: chain E residue 1143 VAL Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU 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 128 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 668 ASN ** E 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.175518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128788 restraints weight = 18806.321| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.23 r_work: 0.3104 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1019 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= 0.216 Angle : 0.840 14.233 20190 Z= 0.394 Chirality : 0.070 0.880 2328 Planarity : 0.004 0.061 2034 Dihedral : 17.051 179.581 3171 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.22 % Allowed : 26.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.23), residues: 1303 helix: 0.46 (0.22), residues: 619 sheet: 0.59 (0.57), residues: 93 loop : -2.31 (0.22), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 400 TYR 0.015 0.002 TYR E 5 PHE 0.022 0.002 PHE E 966 TRP 0.009 0.001 TRP E 659 HIS 0.007 0.002 HIS E 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (14485) covalent geometry : angle 0.84013 / 0.39 (20190) hydrogen bonds : bond 0.08050 / 5.35 ( 507) hydrogen bonds : angle 4.30691 / 2.99 ( 1377) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: E 274 ASP cc_start: 0.7756 (m-30) cc_final: 0.7526 (m-30) REVERT: E 397 ASP cc_start: 0.7245 (m-30) cc_final: 0.6924 (m-30) REVERT: E 494 ARG cc_start: 0.8302 (mtp-110) cc_final: 0.7982 (mtm180) REVERT: E 745 ASP cc_start: 0.7574 (m-30) cc_final: 0.7213 (m-30) REVERT: E 904 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5287 (mp0) REVERT: E 1166 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8090 (mm) REVERT: E 1206 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7012 (mp) REVERT: E 1334 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.7421 (tmtt) outliers start: 38 outliers final: 23 residues processed: 212 average time/residue: 0.1480 time to fit residues: 43.6720 Evaluate side-chains 216 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 479 GLU 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 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 842 VAL Chi-restraints excluded: chain E residue 904 GLU Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 1085 LYS Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1143 VAL Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1166 ILE Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 1226 LEU Chi-restraints excluded: chain E residue 1297 HIS Chi-restraints excluded: chain E residue 1327 PHE Chi-restraints excluded: chain E residue 1334 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 125 optimal weight: 0.1980 chunk 73 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 80 optimal weight: 30.0000 chunk 21 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 295 ASN ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 979 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.178311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.130381 restraints weight = 18891.532| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.06 r_work: 0.3178 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14485 Z= 0.140 Angle : 0.730 12.422 20190 Z= 0.344 Chirality : 0.061 0.726 2328 Planarity : 0.004 0.053 2034 Dihedral : 17.003 179.780 3171 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.46 % Allowed : 26.61 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.23), residues: 1303 helix: 0.75 (0.22), residues: 617 sheet: 0.50 (0.55), residues: 97 loop : -2.29 (0.22), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 340 TYR 0.014 0.001 TYR E 325 PHE 0.016 0.001 PHE E 966 TRP 0.006 0.001 TRP E 659 HIS 0.004 0.001 HIS E 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (14485) covalent geometry : angle 0.72952 / 0.34 (20190) hydrogen bonds : bond 0.05756 / 3.81 ( 507) hydrogen bonds : angle 4.09900 / 2.86 ( 1377) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: E 274 ASP cc_start: 0.7760 (m-30) cc_final: 0.7519 (m-30) REVERT: E 279 LEU cc_start: 0.8014 (tp) cc_final: 0.7811 (mp) REVERT: E 635 ARG cc_start: 0.8281 (tpp80) cc_final: 0.8050 (tpt-90) REVERT: E 745 ASP cc_start: 0.7509 (m-30) cc_final: 0.7152 (m-30) REVERT: E 897 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6731 (p90) REVERT: E 904 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5267 (mp0) REVERT: E 1188 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7853 (mttm) REVERT: E 1334 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.7402 (tmtt) outliers start: 29 outliers final: 17 residues processed: 205 average time/residue: 0.1454 time to fit residues: 41.5625 Evaluate side-chains 208 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 483 ASP 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 642 LEU Chi-restraints excluded: chain E residue 657 THR Chi-restraints excluded: chain E residue 706 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 1065 THR Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1219 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 50.0000 chunk 126 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 0.0570 chunk 102 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 668 ASN E 979 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.176484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130148 restraints weight = 18854.193| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.12 r_work: 0.3141 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14485 Z= 0.190 Angle : 0.765 12.772 20190 Z= 0.362 Chirality : 0.061 0.647 2328 Planarity : 0.004 0.060 2034 Dihedral : 17.014 179.931 3171 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.14 % Allowed : 26.36 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.23), residues: 1303 helix: 0.77 (0.22), residues: 611 sheet: 0.77 (0.57), residues: 91 loop : -2.25 (0.22), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 340 TYR 0.014 0.002 TYR E 5 PHE 0.021 0.002 PHE E 966 TRP 0.008 0.002 TRP E 883 HIS 0.006 0.001 HIS E 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (14485) covalent geometry : angle 0.76461 / 0.36 (20190) hydrogen bonds : bond 0.07115 / 4.73 ( 507) hydrogen bonds : angle 4.14233 / 2.89 ( 1377) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: E 494 ARG cc_start: 0.8274 (mtp-110) cc_final: 0.8014 (mtm180) REVERT: E 601 ILE cc_start: 0.8143 (tp) cc_final: 0.7929 (tp) REVERT: E 635 ARG cc_start: 0.8297 (tpp80) cc_final: 0.8063 (tpt-90) REVERT: E 745 ASP cc_start: 0.7544 (m-30) cc_final: 0.7182 (m-30) REVERT: E 897 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6714 (p90) REVERT: E 904 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5276 (mp0) REVERT: E 1166 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8059 (mm) REVERT: E 1206 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.6946 (mp) REVERT: E 1334 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.7408 (tmtt) REVERT: E 1347 LEU cc_start: 0.8389 (tp) cc_final: 0.8096 (tp) outliers start: 37 outliers final: 26 residues processed: 213 average time/residue: 0.1391 time to fit residues: 41.5567 Evaluate side-chains 222 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 479 GLU 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 642 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 657 THR Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 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 958 LEU Chi-restraints excluded: chain E residue 997 LEU Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1138 THR Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1166 ILE Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 1219 GLU Chi-restraints excluded: chain E residue 1297 HIS Chi-restraints excluded: chain E residue 1327 PHE Chi-restraints excluded: chain E residue 1330 THR Chi-restraints excluded: chain E residue 1334 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 76 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 80 optimal weight: 40.0000 chunk 11 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 940 ASN ** E 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 990 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.174953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127937 restraints weight = 18673.211| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.09 r_work: 0.3109 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14485 Z= 0.233 Angle : 0.823 12.510 20190 Z= 0.389 Chirality : 0.065 0.639 2328 Planarity : 0.005 0.059 2034 Dihedral : 17.090 179.857 3171 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.98 % Allowed : 24.83 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.23), residues: 1303 helix: 0.70 (0.22), residues: 605 sheet: 0.70 (0.56), residues: 91 loop : -2.29 (0.22), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 340 TYR 0.016 0.002 TYR E 5 PHE 0.024 0.002 PHE E 966 TRP 0.007 0.002 TRP E 659 HIS 0.008 0.002 HIS E 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.23 (14485) covalent geometry : angle 0.82292 / 0.39 (20190) hydrogen bonds : bond 0.08255 / 5.49 ( 507) hydrogen bonds : angle 4.25421 / 2.96 ( 1377) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: E 397 ASP cc_start: 0.7189 (m-30) cc_final: 0.6815 (m-30) REVERT: E 494 ARG cc_start: 0.8286 (mtp-110) cc_final: 0.7866 (mtm180) REVERT: E 601 ILE cc_start: 0.8203 (tp) cc_final: 0.7921 (tp) REVERT: E 635 ARG cc_start: 0.8292 (tpp80) cc_final: 0.8064 (tpt-90) REVERT: E 745 ASP cc_start: 0.7551 (m-30) cc_final: 0.7192 (m-30) REVERT: E 897 PHE cc_start: 0.7187 (OUTLIER) cc_final: 0.6699 (p90) REVERT: E 904 GLU cc_start: 0.6227 (OUTLIER) cc_final: 0.5397 (mp0) REVERT: E 1005 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6599 (mp0) REVERT: E 1166 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8052 (mm) REVERT: E 1206 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7014 (mp) REVERT: E 1334 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.7408 (tmtt) REVERT: E 1347 LEU cc_start: 0.8372 (tp) cc_final: 0.8087 (tp) outliers start: 47 outliers final: 35 residues processed: 223 average time/residue: 0.1420 time to fit residues: 44.3975 Evaluate side-chains 231 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 479 GLU 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 642 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain E residue 706 GLU 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 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 940 ASN Chi-restraints excluded: chain E residue 958 LEU Chi-restraints excluded: chain E residue 997 LEU 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 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 1219 GLU Chi-restraints excluded: chain E residue 1226 LEU Chi-restraints excluded: chain E residue 1297 HIS Chi-restraints excluded: chain E residue 1327 PHE Chi-restraints excluded: chain E residue 1330 THR Chi-restraints excluded: chain E residue 1334 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 36 optimal weight: 0.8980 chunk 111 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 123 optimal weight: 0.5980 chunk 80 optimal weight: 30.0000 chunk 28 optimal weight: 0.4980 chunk 83 optimal weight: 50.0000 chunk 69 optimal weight: 0.9990 chunk 88 optimal weight: 30.0000 chunk 35 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 940 ASN E 979 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.178329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.132611 restraints weight = 18671.719| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.04 r_work: 0.3185 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14485 Z= 0.136 Angle : 0.713 12.455 20190 Z= 0.340 Chirality : 0.058 0.489 2328 Planarity : 0.004 0.056 2034 Dihedral : 17.098 179.623 3171 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.14 % Allowed : 25.68 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.23), residues: 1303 helix: 0.92 (0.22), residues: 605 sheet: 0.69 (0.56), residues: 93 loop : -2.23 (0.22), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 340 TYR 0.016 0.001 TYR E 325 PHE 0.013 0.001 PHE E 966 TRP 0.008 0.001 TRP E 883 HIS 0.004 0.001 HIS E 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (14485) covalent geometry : angle 0.71291 / 0.34 (20190) hydrogen bonds : bond 0.05938 / 3.95 ( 507) hydrogen bonds : angle 4.08021 / 2.85 ( 1377) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: E 174 LEU cc_start: 0.8099 (tp) cc_final: 0.7897 (mp) REVERT: E 601 ILE cc_start: 0.8289 (tp) cc_final: 0.7989 (tp) REVERT: E 635 ARG cc_start: 0.8419 (tpp80) cc_final: 0.8184 (tpt-90) REVERT: E 745 ASP cc_start: 0.7796 (m-30) cc_final: 0.7452 (m-30) REVERT: E 897 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6703 (p90) REVERT: E 904 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5360 (mp0) REVERT: E 1005 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6902 (mp0) REVERT: E 1188 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7956 (mttm) REVERT: E 1206 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7006 (mp) REVERT: E 1334 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.7470 (tmtt) REVERT: E 1347 LEU cc_start: 0.8482 (tp) cc_final: 0.8207 (tp) outliers start: 37 outliers final: 24 residues processed: 214 average time/residue: 0.1430 time to fit residues: 42.7240 Evaluate side-chains 218 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 109 GLU 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 578 VAL Chi-restraints excluded: chain E residue 597 LEU Chi-restraints excluded: chain E residue 604 LYS Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 841 ILE Chi-restraints excluded: chain E residue 842 VAL Chi-restraints excluded: chain E residue 897 PHE Chi-restraints excluded: chain E residue 904 GLU Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 940 ASN Chi-restraints excluded: chain E residue 958 LEU Chi-restraints excluded: chain E residue 1065 THR Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 1219 GLU Chi-restraints excluded: chain E residue 1297 HIS Chi-restraints excluded: chain E residue 1327 PHE Chi-restraints excluded: chain E residue 1330 THR Chi-restraints excluded: chain E residue 1334 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 0.0040 chunk 58 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 117 optimal weight: 0.1980 chunk 56 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 940 ASN E 979 ASN E 990 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.175398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127628 restraints weight = 18618.986| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.02 r_work: 0.3116 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1648 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= 0.232 Angle : 0.802 13.218 20190 Z= 0.378 Chirality : 0.063 0.570 2328 Planarity : 0.004 0.056 2034 Dihedral : 17.101 179.770 3171 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.31 % Allowed : 25.17 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.23), residues: 1303 helix: 0.83 (0.22), residues: 605 sheet: 0.73 (0.56), residues: 91 loop : -2.29 (0.22), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 340 TYR 0.015 0.002 TYR E 5 PHE 0.024 0.002 PHE E 966 TRP 0.007 0.002 TRP E 659 HIS 0.008 0.002 HIS E 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (14485) covalent geometry : angle 0.80211 / 0.38 (20190) hydrogen bonds : bond 0.07759 / 5.17 ( 507) hydrogen bonds : angle 4.16317 / 2.91 ( 1377) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: E 174 LEU cc_start: 0.8039 (tp) cc_final: 0.7833 (mp) REVERT: E 601 ILE cc_start: 0.8222 (tp) cc_final: 0.7914 (tp) REVERT: E 635 ARG cc_start: 0.8308 (tpp80) cc_final: 0.8078 (tpt-90) REVERT: E 745 ASP cc_start: 0.7543 (m-30) cc_final: 0.7177 (m-30) REVERT: E 897 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6690 (p90) REVERT: E 904 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.5389 (mp0) REVERT: E 1005 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6597 (mp0) REVERT: E 1166 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8037 (mm) REVERT: E 1188 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7853 (mttm) REVERT: E 1206 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.6993 (mp) REVERT: E 1268 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: E 1334 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.7409 (tmtt) REVERT: E 1347 LEU cc_start: 0.8365 (tp) cc_final: 0.8083 (tp) outliers start: 39 outliers final: 32 residues processed: 216 average time/residue: 0.1422 time to fit residues: 43.0944 Evaluate side-chains 228 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN 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 479 GLU 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 642 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 650 GLN 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 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 940 ASN Chi-restraints excluded: chain E residue 958 LEU Chi-restraints excluded: chain E residue 997 LEU Chi-restraints excluded: chain E residue 1065 THR Chi-restraints excluded: chain E residue 1085 LYS Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1138 THR Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1166 ILE Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 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 132 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 100 optimal weight: 0.0470 chunk 137 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 80 optimal weight: 30.0000 chunk 69 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 940 ASN ** E 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 990 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.177529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131620 restraints weight = 18742.031| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.12 r_work: 0.3167 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14485 Z= 0.143 Angle : 0.717 12.204 20190 Z= 0.340 Chirality : 0.057 0.435 2328 Planarity : 0.004 0.056 2034 Dihedral : 17.094 179.825 3168 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.97 % Allowed : 25.76 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.23), residues: 1303 helix: 0.97 (0.22), residues: 605 sheet: 0.59 (0.56), residues: 93 loop : -2.25 (0.22), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 340 TYR 0.014 0.001 TYR E 325 PHE 0.015 0.001 PHE E 966 TRP 0.006 0.001 TRP E 659 HIS 0.004 0.001 HIS E 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (14485) covalent geometry : angle 0.71661 / 0.34 (20190) hydrogen bonds : bond 0.06051 / 4.03 ( 507) hydrogen bonds : angle 4.05669 / 2.83 ( 1377) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: E 467 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8255 (mtt90) REVERT: E 601 ILE cc_start: 0.8192 (tp) cc_final: 0.7882 (tp) REVERT: E 635 ARG cc_start: 0.8294 (tpp80) cc_final: 0.8058 (tpt-90) REVERT: E 745 ASP cc_start: 0.7493 (m-30) cc_final: 0.7120 (m-30) REVERT: E 897 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6715 (p90) REVERT: E 904 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5403 (mp0) REVERT: E 1005 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6577 (mp0) REVERT: E 1166 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8051 (mm) REVERT: E 1188 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7847 (mttm) REVERT: E 1206 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6883 (mp) REVERT: E 1334 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.7397 (tmtt) REVERT: E 1347 LEU cc_start: 0.8344 (tp) cc_final: 0.8074 (tp) outliers start: 35 outliers final: 26 residues processed: 215 average time/residue: 0.1353 time to fit residues: 40.5294 Evaluate side-chains 223 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 109 GLU 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 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 657 THR Chi-restraints excluded: chain E residue 743 VAL Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 841 ILE Chi-restraints excluded: chain E residue 842 VAL Chi-restraints excluded: chain E residue 897 PHE Chi-restraints excluded: chain E residue 904 GLU Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 940 ASN Chi-restraints excluded: chain E residue 958 LEU Chi-restraints excluded: chain E residue 1065 THR Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1138 THR Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1166 ILE Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 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 60 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 24 optimal weight: 0.0060 chunk 52 optimal weight: 4.9990 chunk 88 optimal weight: 50.0000 chunk 104 optimal weight: 4.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 940 ASN E 979 ASN E 990 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.176466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129863 restraints weight = 18713.405| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.10 r_work: 0.3148 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14485 Z= 0.186 Angle : 0.750 12.975 20190 Z= 0.355 Chirality : 0.059 0.482 2328 Planarity : 0.004 0.057 2034 Dihedral : 17.106 179.809 3168 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.88 % Allowed : 26.02 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.23), residues: 1303 helix: 0.91 (0.22), residues: 610 sheet: 0.69 (0.56), residues: 91 loop : -2.29 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 340 TYR 0.013 0.001 TYR E 5 PHE 0.020 0.002 PHE E 966 TRP 0.007 0.001 TRP E 659 HIS 0.006 0.001 HIS E 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (14485) covalent geometry : angle 0.75038 / 0.35 (20190) hydrogen bonds : bond 0.06863 / 4.57 ( 507) hydrogen bonds : angle 4.07807 / 2.85 ( 1377) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: E 467 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8438 (mtt90) REVERT: E 601 ILE cc_start: 0.8278 (tp) cc_final: 0.7980 (tp) REVERT: E 635 ARG cc_start: 0.8440 (tpp80) cc_final: 0.8205 (tpt-90) REVERT: E 745 ASP cc_start: 0.7813 (m-30) cc_final: 0.7455 (m-30) REVERT: E 897 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6713 (p90) REVERT: E 904 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5426 (mp0) REVERT: E 1005 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6843 (mp0) REVERT: E 1166 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8107 (mm) REVERT: E 1188 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7934 (mttm) REVERT: E 1206 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7046 (mp) REVERT: E 1334 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.7507 (tmtt) REVERT: E 1347 LEU cc_start: 0.8474 (tp) cc_final: 0.8201 (tp) outliers start: 34 outliers final: 25 residues processed: 214 average time/residue: 0.1441 time to fit residues: 43.0777 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 : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN 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 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 657 THR Chi-restraints excluded: chain E residue 743 VAL Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 841 ILE Chi-restraints excluded: chain E residue 842 VAL Chi-restraints excluded: chain E residue 897 PHE Chi-restraints excluded: chain E residue 904 GLU Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 958 LEU Chi-restraints excluded: chain E residue 1065 THR Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1138 THR Chi-restraints excluded: chain E residue 1146 VAL Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1166 ILE Chi-restraints excluded: chain E residue 1188 LYS Chi-restraints excluded: chain E residue 1206 LEU Chi-restraints excluded: chain E residue 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 129 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 143 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 81 optimal weight: 50.0000 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 940 ASN ** E 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.176615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130699 restraints weight = 18627.609| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.11 r_work: 0.3143 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14485 Z= 0.177 Angle : 0.739 12.870 20190 Z= 0.351 Chirality : 0.058 0.469 2328 Planarity : 0.004 0.057 2034 Dihedral : 17.178 179.902 3168 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.88 % Allowed : 25.93 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.23), residues: 1303 helix: 0.92 (0.22), residues: 612 sheet: 0.65 (0.56), residues: 91 loop : -2.27 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 340 TYR 0.012 0.001 TYR E 325 PHE 0.019 0.002 PHE E 966 TRP 0.006 0.001 TRP E 659 HIS 0.006 0.001 HIS E 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (14485) covalent geometry : angle 0.73888 / 0.35 (20190) hydrogen bonds : bond 0.06757 / 4.50 ( 507) hydrogen bonds : angle 4.06489 / 2.84 ( 1377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3929.32 seconds wall clock time: 67 minutes 52.08 seconds (4072.08 seconds total)