Starting phenix.real_space_refine on Wed Aug 5 12:32:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iz9_35836/08_2026/8iz9_35836_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iz9_35836/08_2026/8iz9_35836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iz9_35836/08_2026/8iz9_35836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iz9_35836/08_2026/8iz9_35836.map" model { file = "/net/cci-nas-00/data/ceres_data/8iz9_35836/08_2026/8iz9_35836_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iz9_35836/08_2026/8iz9_35836_trim.cif" } resolution = 2.95 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= 0.004 sd= 0.075 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6351 2.51 5 N 1638 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 9779 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9754 Classifications: {'peptide': 1224} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1185} Chain breaks: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'XPG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.94, per 1000 atoms: 0.20 Number of scatterers: 9779 At special positions: 0 Unit cell: (74.385, 103.455, 153.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1747 8.00 N 1638 7.00 C 6351 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: 0.84 Conformation dependent library (CDL) restraints added in 232.9 milliseconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 3 sheets defined 70.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.575A pdb=" N LYS A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 removed outlier: 3.516A pdb=" N ASP A 43 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET A 44 " --> pdb=" O GLU A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 44' Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 74 removed outlier: 3.622A pdb=" N LEU A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 122 removed outlier: 5.801A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.602A pdb=" N TYR A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 179 removed outlier: 3.817A pdb=" N LEU A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 Processing helix chain 'A' and resid 190 through 213 removed outlier: 3.501A pdb=" N ILE A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N HIS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 234 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 236 through 282 removed outlier: 4.420A pdb=" N GLY A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.769A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.546A pdb=" N ILE A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 343 removed outlier: 4.067A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 391 removed outlier: 4.092A pdb=" N PHE A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Proline residue: A 370 - end of helix Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.683A pdb=" N LEU A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.983A pdb=" N THR A 526 " --> pdb=" O GLY A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 550 Processing helix chain 'A' and resid 566 through 578 Processing helix chain 'A' and resid 581 through 585 removed outlier: 4.316A pdb=" N GLU A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.524A pdb=" N LEU A 597 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 Processing helix chain 'A' and resid 697 through 709 removed outlier: 4.018A pdb=" N TYR A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 751 removed outlier: 3.922A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 807 removed outlier: 3.602A pdb=" N TYR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 4.092A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 861 removed outlier: 3.914A pdb=" N ASP A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Proline residue: A 837 - end of helix Processing helix chain 'A' and resid 862 through 866 removed outlier: 3.894A pdb=" N ALA A 865 " --> pdb=" O PRO A 862 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 866 " --> pdb=" O TRP A 863 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 862 through 866' Processing helix chain 'A' and resid 867 through 910 removed outlier: 3.940A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix removed outlier: 3.547A pdb=" N GLY A 910 " --> pdb=" O SER A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 918 Processing helix chain 'A' and resid 919 through 970 removed outlier: 4.057A pdb=" N CYS A 923 " --> pdb=" O ALA A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 removed outlier: 3.797A pdb=" N LEU A 974 " --> pdb=" O ALA A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 975 through 987 Processing helix chain 'A' and resid 991 through 1018 removed outlier: 4.436A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1090 Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1153 removed outlier: 4.294A pdb=" N LEU A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 removed outlier: 3.718A pdb=" N ILE A1159 " --> pdb=" O LEU A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1193 Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1258 through 1264 removed outlier: 3.597A pdb=" N ASN A1264 " --> pdb=" O VAL A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1276 removed outlier: 3.893A pdb=" N LYS A1271 " --> pdb=" O SER A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1297 removed outlier: 3.513A pdb=" N TYR A1297 " --> pdb=" O PHE A1293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 475 through 477 removed outlier: 4.383A pdb=" N ALA A 476 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU A 557 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 558 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 590 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU A 441 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 444 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 603 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY A 615 " --> pdb=" O ILE A 603 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1041 through 1042 removed outlier: 4.175A pdb=" N TRP A1099 " --> pdb=" O ILE A1042 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1228 through 1232 removed outlier: 6.486A pdb=" N VAL A1071 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA A1232 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A1073 " --> pdb=" O ALA A1232 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N MET A1245 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A1074 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU A1247 " --> pdb=" O VAL A1074 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP A1256 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A1246 " --> pdb=" O GLU A1254 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU A1254 " --> pdb=" O VAL A1246 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1806 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1616 1.32 - 1.45: 2596 1.45 - 1.57: 5705 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 9987 Sorted by residual: bond pdb=" C13 XPG A1401 " pdb=" C14 XPG A1401 " ideal model delta sigma weight residual 1.328 1.292 0.036 2.00e-02 2.50e+03 3.30e+00 bond pdb=" C18 XPG A1401 " pdb=" C19 XPG A1401 " ideal model delta sigma weight residual 1.524 1.497 0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C2 XPG A1401 " pdb=" C3 XPG A1401 " ideal model delta sigma weight residual 1.520 1.495 0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" N ASN A1139 " pdb=" CA ASN A1139 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.32e+00 bond pdb=" C17 XPG A1401 " pdb=" C18 XPG A1401 " ideal model delta sigma weight residual 1.524 1.501 0.023 2.00e-02 2.50e+03 1.28e+00 ... (remaining 9982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 13363 2.03 - 4.07: 137 4.07 - 6.10: 29 6.10 - 8.13: 1 8.13 - 10.17: 3 Bond angle restraints: 13533 Sorted by residual: angle pdb=" CA LEU A 13 " pdb=" CB LEU A 13 " pdb=" CG LEU A 13 " ideal model delta sigma weight residual 116.30 126.47 -10.17 3.50e+00 8.16e-02 8.44e+00 angle pdb=" C12 XPG A1401 " pdb=" C8 XPG A1401 " pdb=" C7 XPG A1401 " ideal model delta sigma weight residual 114.63 123.33 -8.70 3.00e+00 1.11e-01 8.42e+00 angle pdb=" C7 XPG A1401 " pdb=" C8 XPG A1401 " pdb=" C9 XPG A1401 " ideal model delta sigma weight residual 115.09 106.64 8.45 3.00e+00 1.11e-01 7.92e+00 angle pdb=" N LYS A1156 " pdb=" CA LYS A1156 " pdb=" C LYS A1156 " ideal model delta sigma weight residual 111.36 113.96 -2.60 1.09e+00 8.42e-01 5.68e+00 angle pdb=" N GLY A1072 " pdb=" CA GLY A1072 " pdb=" C GLY A1072 " ideal model delta sigma weight residual 111.46 115.55 -4.09 1.75e+00 3.27e-01 5.46e+00 ... (remaining 13528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.80: 5420 18.80 - 37.61: 458 37.61 - 56.41: 70 56.41 - 75.21: 19 75.21 - 94.02: 11 Dihedral angle restraints: 5978 sinusoidal: 2407 harmonic: 3571 Sorted by residual: dihedral pdb=" CA ASP A1212 " pdb=" CB ASP A1212 " pdb=" CG ASP A1212 " pdb=" OD1 ASP A1212 " ideal model delta sinusoidal sigma weight residual -30.00 -89.05 59.05 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" C15 XPG A1401 " pdb=" C16 XPG A1401 " pdb=" C17 XPG A1401 " pdb=" C18 XPG A1401 " ideal model delta sinusoidal sigma weight residual -176.15 -82.13 -94.02 1 3.00e+01 1.11e-03 1.14e+01 dihedral pdb=" CB LYS A1194 " pdb=" CG LYS A1194 " pdb=" CD LYS A1194 " pdb=" CE LYS A1194 " ideal model delta sinusoidal sigma weight residual 60.00 117.92 -57.92 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1124 0.036 - 0.072: 352 0.072 - 0.108: 79 0.108 - 0.144: 17 0.144 - 0.180: 1 Chirality restraints: 1573 Sorted by residual: chirality pdb=" CB VAL A1153 " pdb=" CA VAL A1153 " pdb=" CG1 VAL A1153 " pdb=" CG2 VAL A1153 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" C15 XPG A1401 " pdb=" C14 XPG A1401 " pdb=" C16 XPG A1401 " pdb=" O15 XPG A1401 " both_signs ideal model delta sigma weight residual False 2.25 2.39 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE A1073 " pdb=" N ILE A1073 " pdb=" C ILE A1073 " pdb=" CB ILE A1073 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 1570 not shown) Planarity restraints: 1682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 XPG A1401 " 0.101 2.00e-02 2.50e+03 2.09e-01 4.36e+02 pdb=" C13 XPG A1401 " -0.285 2.00e-02 2.50e+03 pdb=" C14 XPG A1401 " 0.274 2.00e-02 2.50e+03 pdb=" C15 XPG A1401 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 11 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO A 12 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 12 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 12 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 898 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 899 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 899 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 899 " 0.015 5.00e-02 4.00e+02 ... (remaining 1679 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2439 2.80 - 3.32: 9552 3.32 - 3.85: 16149 3.85 - 4.37: 17170 4.37 - 4.90: 30635 Nonbonded interactions: 75945 Sorted by model distance: nonbonded pdb=" OG1 THR A 269 " pdb=" OE2 GLU A 306 " model vdw 2.273 3.040 nonbonded pdb=" NE2 HIS A 153 " pdb=" OD2 ASP A 953 " model vdw 2.285 3.120 nonbonded pdb=" O GLY A 450 " pdb=" OG SER A 453 " model vdw 2.286 3.040 nonbonded pdb=" O VAL A 484 " pdb=" OG SER A 906 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR A 504 " pdb=" OD2 ASP A 524 " model vdw 2.308 3.040 ... (remaining 75940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 8.430 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 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 : 0.002 0.036 9987 Z= 0.126 Angle : 0.562 10.169 13533 Z= 0.310 Chirality : 0.037 0.180 1573 Planarity : 0.006 0.209 1682 Dihedral : 14.569 94.017 3666 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.94 (0.23), residues: 1218 helix: 0.38 (0.18), residues: 784 sheet: -1.45 (0.81), residues: 37 loop : -2.59 (0.26), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 317 TYR 0.017 0.001 TYR A1270 PHE 0.006 0.001 PHE A1043 TRP 0.008 0.001 TRP A 763 HIS 0.003 0.000 HIS A 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.13 ( 9987) covalent geometry : angle 0.56150 / 0.31 (13533) hydrogen bonds : bond 0.10781 / 7.15 ( 608) hydrogen bonds : angle 4.24158 / 2.98 ( 1806) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1145 GLU cc_start: 0.6429 (mp0) cc_final: 0.6208 (pm20) outliers start: 0 outliers final: 2 residues processed: 137 average time/residue: 0.5262 time to fit residues: 77.1884 Evaluate side-chains 82 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 380 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.0570 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 113 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 54.7229 > 50:) chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 HIS A 213 HIS A 297 ASN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 ASN A 931 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1275 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.234081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.165989 restraints weight = 11279.112| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.07 r_work: 0.3757 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 9987 Z= 0.251 Angle : 0.824 12.667 13533 Z= 0.420 Chirality : 0.050 0.227 1573 Planarity : 0.005 0.056 1682 Dihedral : 5.601 78.841 1355 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.54 % Allowed : 13.33 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.27 (0.23), residues: 1218 helix: 0.73 (0.18), residues: 797 sheet: -1.02 (0.73), residues: 44 loop : -2.00 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 824 TYR 0.034 0.003 TYR A1016 PHE 0.033 0.003 PHE A 352 TRP 0.063 0.003 TRP A1025 HIS 0.024 0.003 HIS A1111 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.25 ( 9987) covalent geometry : angle 0.82398 / 0.42 (13533) hydrogen bonds : bond 0.09868 / 6.32 ( 608) hydrogen bonds : angle 4.42200 / 3.14 ( 1806) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.6408 (pm20) cc_final: 0.6040 (pm20) REVERT: A 143 PHE cc_start: 0.7211 (t80) cc_final: 0.6979 (m-10) REVERT: A 164 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.8004 (ttp) REVERT: A 186 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5823 (mmm) REVERT: A 196 ASN cc_start: 0.6667 (OUTLIER) cc_final: 0.6401 (m110) REVERT: A 232 GLU cc_start: 0.8078 (tp30) cc_final: 0.7773 (tt0) REVERT: A 270 ASP cc_start: 0.6957 (m-30) cc_final: 0.6282 (m-30) REVERT: A 274 ARG cc_start: 0.7503 (ttp-170) cc_final: 0.7135 (mtp180) REVERT: A 716 PHE cc_start: 0.6758 (m-80) cc_final: 0.6479 (m-80) REVERT: A 958 MET cc_start: 0.8292 (tpp) cc_final: 0.7861 (ttp) REVERT: A 1002 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: A 1015 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7872 (tt0) REVERT: A 1047 ASN cc_start: 0.3748 (m-40) cc_final: 0.3302 (m-40) outliers start: 27 outliers final: 6 residues processed: 111 average time/residue: 0.5470 time to fit residues: 65.3231 Evaluate side-chains 85 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1245 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 22 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 429 GLN ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.235237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.166617 restraints weight = 11167.208| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.02 r_work: 0.3711 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9987 Z= 0.148 Angle : 0.564 12.935 13533 Z= 0.284 Chirality : 0.040 0.149 1573 Planarity : 0.004 0.056 1682 Dihedral : 4.730 82.867 1351 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.97 % Allowed : 17.37 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 (0.24), residues: 1218 helix: 1.54 (0.19), residues: 791 sheet: -0.84 (0.75), residues: 44 loop : -1.70 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1189 TYR 0.012 0.001 TYR A 155 PHE 0.020 0.001 PHE A 336 TRP 0.024 0.002 TRP A 947 HIS 0.007 0.001 HIS A1111 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 9987) covalent geometry : angle 0.56375 / 0.28 (13533) hydrogen bonds : bond 0.07313 / 4.69 ( 608) hydrogen bonds : angle 3.80566 / 2.71 ( 1806) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.7248 (p0) cc_final: 0.6989 (p0) REVERT: A 76 GLN cc_start: 0.6735 (pm20) cc_final: 0.6394 (pm20) REVERT: A 270 ASP cc_start: 0.7097 (m-30) cc_final: 0.6616 (m-30) REVERT: A 274 ARG cc_start: 0.7518 (ttp-170) cc_final: 0.7144 (mtp180) REVERT: A 556 TYR cc_start: 0.6478 (m-80) cc_final: 0.6035 (m-80) REVERT: A 803 GLU cc_start: 0.7547 (tp30) cc_final: 0.7102 (mp0) REVERT: A 834 ASP cc_start: 0.7456 (m-30) cc_final: 0.7226 (t70) REVERT: A 936 GLU cc_start: 0.7142 (tt0) cc_final: 0.6920 (tt0) REVERT: A 972 LYS cc_start: 0.8093 (mttt) cc_final: 0.7851 (mttp) REVERT: A 1002 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: A 1049 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6267 (mpt) outliers start: 21 outliers final: 6 residues processed: 92 average time/residue: 0.6132 time to fit residues: 60.3745 Evaluate side-chains 75 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1245 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 111 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 ASN A 903 HIS ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.230308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.160309 restraints weight = 11232.926| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.01 r_work: 0.3606 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9987 Z= 0.150 Angle : 0.569 12.153 13533 Z= 0.288 Chirality : 0.041 0.150 1573 Planarity : 0.004 0.058 1682 Dihedral : 4.437 71.739 1351 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.82 % Allowed : 18.69 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 (0.24), residues: 1218 helix: 1.80 (0.19), residues: 785 sheet: -0.58 (0.75), residues: 44 loop : -1.53 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 815 TYR 0.013 0.001 TYR A 155 PHE 0.021 0.001 PHE A 336 TRP 0.023 0.001 TRP A 947 HIS 0.007 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 ( 9987) covalent geometry : angle 0.56876 / 0.29 (13533) hydrogen bonds : bond 0.07403 / 4.72 ( 608) hydrogen bonds : angle 3.72447 / 2.68 ( 1806) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 65 ASP cc_start: 0.7264 (p0) cc_final: 0.6855 (m-30) REVERT: A 76 GLN cc_start: 0.6725 (pm20) cc_final: 0.6319 (pm20) REVERT: A 184 MET cc_start: 0.6721 (mpp) cc_final: 0.6352 (mpt) REVERT: A 196 ASN cc_start: 0.7112 (OUTLIER) cc_final: 0.6753 (m110) REVERT: A 274 ARG cc_start: 0.7539 (ttp-170) cc_final: 0.7147 (mtp180) REVERT: A 409 MET cc_start: 0.5166 (tmm) cc_final: 0.4962 (mtp) REVERT: A 556 TYR cc_start: 0.6939 (m-80) cc_final: 0.6412 (m-80) REVERT: A 719 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7480 (mt) REVERT: A 744 MET cc_start: 0.6645 (tmm) cc_final: 0.6162 (ttm) REVERT: A 803 GLU cc_start: 0.7633 (tp30) cc_final: 0.7017 (mp0) REVERT: A 936 GLU cc_start: 0.7333 (tt0) cc_final: 0.6931 (tt0) REVERT: A 958 MET cc_start: 0.8362 (tpt) cc_final: 0.7876 (ttp) REVERT: A 972 LYS cc_start: 0.8263 (mttt) cc_final: 0.7981 (mttp) REVERT: A 1002 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: A 1049 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.6276 (mpt) REVERT: A 1112 ASP cc_start: 0.6918 (t70) cc_final: 0.6655 (t0) REVERT: A 1166 MET cc_start: 0.3999 (tpt) cc_final: 0.3797 (tpp) REVERT: A 1181 GLN cc_start: 0.2772 (OUTLIER) cc_final: 0.2508 (pp30) outliers start: 30 outliers final: 9 residues processed: 91 average time/residue: 0.5870 time to fit residues: 57.7268 Evaluate side-chains 77 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1181 GLN Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 18 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 0.0570 chunk 11 optimal weight: 0.0040 chunk 34 optimal weight: 1.9990 overall best weight: 0.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 HIS A 213 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.234151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.165337 restraints weight = 11115.499| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.24 r_work: 0.3663 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9987 Z= 0.123 Angle : 0.510 11.508 13533 Z= 0.258 Chirality : 0.039 0.255 1573 Planarity : 0.004 0.090 1682 Dihedral : 4.221 62.972 1351 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.72 % Allowed : 18.97 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.47 (0.25), residues: 1218 helix: 2.14 (0.19), residues: 785 sheet: -0.33 (0.76), residues: 49 loop : -1.40 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1295 TYR 0.010 0.001 TYR A 737 PHE 0.009 0.001 PHE A 336 TRP 0.023 0.001 TRP A 947 HIS 0.005 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 ( 9987) covalent geometry : angle 0.51041 / 0.26 (13533) hydrogen bonds : bond 0.06164 / 3.92 ( 608) hydrogen bonds : angle 3.55675 / 2.57 ( 1806) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.7440 (p0) cc_final: 0.6974 (m-30) REVERT: A 76 GLN cc_start: 0.6876 (pm20) cc_final: 0.6405 (pm20) REVERT: A 184 MET cc_start: 0.6712 (mpp) cc_final: 0.6400 (mpt) REVERT: A 274 ARG cc_start: 0.7596 (ttp-170) cc_final: 0.7279 (mtp180) REVERT: A 556 TYR cc_start: 0.6893 (m-80) cc_final: 0.6435 (m-80) REVERT: A 744 MET cc_start: 0.6716 (tmm) cc_final: 0.6258 (ttm) REVERT: A 803 GLU cc_start: 0.7717 (tp30) cc_final: 0.7064 (mp0) REVERT: A 936 GLU cc_start: 0.7093 (tt0) cc_final: 0.6564 (tt0) REVERT: A 972 LYS cc_start: 0.8202 (mttt) cc_final: 0.7951 (mttp) REVERT: A 1002 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: A 1112 ASP cc_start: 0.6920 (t70) cc_final: 0.6658 (t0) REVERT: A 1181 GLN cc_start: 0.2691 (OUTLIER) cc_final: 0.2434 (pp30) outliers start: 29 outliers final: 6 residues processed: 88 average time/residue: 0.5725 time to fit residues: 54.5115 Evaluate side-chains 71 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1181 GLN Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 100 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 59 optimal weight: 0.0470 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 GLN ** 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 = 0.4700 r_free = 0.4700 target = 0.234355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.163375 restraints weight = 11501.785| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 3.78 r_work: 0.3821 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9987 Z= 0.128 Angle : 0.536 11.674 13533 Z= 0.264 Chirality : 0.040 0.190 1573 Planarity : 0.003 0.048 1682 Dihedral : 4.028 51.480 1351 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.63 % Allowed : 19.91 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.61 (0.25), residues: 1218 helix: 2.22 (0.19), residues: 786 sheet: -0.17 (0.78), residues: 49 loop : -1.29 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 436 TYR 0.011 0.001 TYR A 737 PHE 0.016 0.001 PHE A 336 TRP 0.021 0.001 TRP A 947 HIS 0.005 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 ( 9987) covalent geometry : angle 0.53604 / 0.26 (13533) hydrogen bonds : bond 0.06441 / 4.11 ( 608) hydrogen bonds : angle 3.53987 / 2.57 ( 1806) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.272 Fit side-chains REVERT: A 65 ASP cc_start: 0.7283 (p0) cc_final: 0.6854 (m-30) REVERT: A 76 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6531 (pm20) REVERT: A 126 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6890 (mtt) REVERT: A 184 MET cc_start: 0.6611 (mpp) cc_final: 0.6368 (mpt) REVERT: A 196 ASN cc_start: 0.7102 (OUTLIER) cc_final: 0.6761 (m110) REVERT: A 274 ARG cc_start: 0.7642 (ttp-170) cc_final: 0.7267 (mtp180) REVERT: A 556 TYR cc_start: 0.6714 (m-80) cc_final: 0.6247 (m-80) REVERT: A 719 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7514 (mt) REVERT: A 744 MET cc_start: 0.6541 (tmm) cc_final: 0.6119 (ttm) REVERT: A 803 GLU cc_start: 0.7382 (tp30) cc_final: 0.6899 (mp0) REVERT: A 936 GLU cc_start: 0.7075 (tt0) cc_final: 0.6722 (tt0) REVERT: A 958 MET cc_start: 0.8280 (tpt) cc_final: 0.7801 (ttp) REVERT: A 972 LYS cc_start: 0.8187 (mttt) cc_final: 0.7943 (mttp) REVERT: A 1157 GLU cc_start: 0.6533 (mp0) cc_final: 0.5434 (tm-30) REVERT: A 1181 GLN cc_start: 0.3034 (OUTLIER) cc_final: 0.2554 (pp30) REVERT: A 1212 ASP cc_start: 0.8359 (m-30) cc_final: 0.7986 (m-30) outliers start: 28 outliers final: 11 residues processed: 85 average time/residue: 0.5229 time to fit residues: 48.2790 Evaluate side-chains 75 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1181 GLN Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 5 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 GLN ** 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 = 0.4645 r_free = 0.4645 target = 0.227901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.162049 restraints weight = 11280.302| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.26 r_work: 0.3759 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9987 Z= 0.160 Angle : 0.579 11.070 13533 Z= 0.294 Chirality : 0.041 0.159 1573 Planarity : 0.004 0.061 1682 Dihedral : 4.109 40.213 1351 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.72 % Allowed : 20.38 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1218 helix: 1.89 (0.19), residues: 791 sheet: -0.14 (0.78), residues: 49 loop : -1.26 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 436 TYR 0.015 0.001 TYR A 289 PHE 0.022 0.002 PHE A 336 TRP 0.024 0.002 TRP A 912 HIS 0.008 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 ( 9987) covalent geometry : angle 0.57912 / 0.29 (13533) hydrogen bonds : bond 0.07816 / 4.99 ( 608) hydrogen bonds : angle 3.75697 / 2.73 ( 1806) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 65 ASP cc_start: 0.7557 (p0) cc_final: 0.7114 (m-30) REVERT: A 196 ASN cc_start: 0.7440 (OUTLIER) cc_final: 0.7098 (m110) REVERT: A 274 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.7363 (mtp180) REVERT: A 556 TYR cc_start: 0.7172 (m-80) cc_final: 0.6608 (m-80) REVERT: A 719 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7708 (mt) REVERT: A 744 MET cc_start: 0.7022 (tmm) cc_final: 0.6642 (ttm) REVERT: A 803 GLU cc_start: 0.7933 (tp30) cc_final: 0.7293 (mp0) REVERT: A 904 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6544 (tp) REVERT: A 936 GLU cc_start: 0.7592 (tt0) cc_final: 0.7247 (tt0) REVERT: A 958 MET cc_start: 0.8500 (tpt) cc_final: 0.8030 (ttp) REVERT: A 972 LYS cc_start: 0.8414 (mttt) cc_final: 0.8066 (mttp) REVERT: A 1002 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: A 1181 GLN cc_start: 0.3053 (OUTLIER) cc_final: 0.2735 (pp30) outliers start: 29 outliers final: 12 residues processed: 89 average time/residue: 0.5447 time to fit residues: 52.5601 Evaluate side-chains 79 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1181 GLN Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 22 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 0.0270 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 213 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.230261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.162063 restraints weight = 11402.033| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 3.26 r_work: 0.3774 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9987 Z= 0.134 Angle : 0.539 11.622 13533 Z= 0.270 Chirality : 0.040 0.176 1573 Planarity : 0.003 0.048 1682 Dihedral : 4.061 39.717 1351 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.07 % Allowed : 20.85 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.54 (0.25), residues: 1218 helix: 2.07 (0.19), residues: 790 sheet: -0.00 (0.78), residues: 49 loop : -1.15 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1189 TYR 0.014 0.001 TYR A 155 PHE 0.013 0.001 PHE A 336 TRP 0.022 0.002 TRP A 947 HIS 0.004 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 9987) covalent geometry : angle 0.53895 / 0.27 (13533) hydrogen bonds : bond 0.06888 / 4.39 ( 608) hydrogen bonds : angle 3.64297 / 2.66 ( 1806) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.354 Fit side-chains REVERT: A 65 ASP cc_start: 0.7306 (p0) cc_final: 0.6855 (m-30) REVERT: A 196 ASN cc_start: 0.7236 (OUTLIER) cc_final: 0.6910 (m110) REVERT: A 274 ARG cc_start: 0.7617 (ttp-170) cc_final: 0.7234 (mtp180) REVERT: A 556 TYR cc_start: 0.6804 (m-80) cc_final: 0.6236 (m-80) REVERT: A 744 MET cc_start: 0.6834 (tmm) cc_final: 0.6473 (ttm) REVERT: A 803 GLU cc_start: 0.7488 (tp30) cc_final: 0.6996 (mp0) REVERT: A 904 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6401 (tp) REVERT: A 936 GLU cc_start: 0.7112 (tt0) cc_final: 0.6769 (tt0) REVERT: A 972 LYS cc_start: 0.8258 (mttt) cc_final: 0.7968 (mttp) REVERT: A 1157 GLU cc_start: 0.6524 (mp0) cc_final: 0.5510 (tm-30) REVERT: A 1181 GLN cc_start: 0.3065 (OUTLIER) cc_final: 0.2669 (pp30) REVERT: A 1212 ASP cc_start: 0.8353 (m-30) cc_final: 0.7949 (m-30) outliers start: 22 outliers final: 10 residues processed: 84 average time/residue: 0.5530 time to fit residues: 50.1646 Evaluate side-chains 76 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1181 GLN Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.9990 chunk 116 optimal weight: 0.0670 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 213 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.224011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.157636 restraints weight = 11188.902| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.27 r_work: 0.3691 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.7203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9987 Z= 0.182 Angle : 0.632 11.768 13533 Z= 0.317 Chirality : 0.043 0.215 1573 Planarity : 0.004 0.047 1682 Dihedral : 4.167 36.384 1351 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.35 % Allowed : 21.03 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.19 (0.24), residues: 1218 helix: 1.77 (0.18), residues: 792 sheet: 0.21 (0.78), residues: 47 loop : -1.28 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 951 TYR 0.017 0.002 TYR A 339 PHE 0.028 0.002 PHE A 336 TRP 0.020 0.002 TRP A 947 HIS 0.009 0.002 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 9987) covalent geometry : angle 0.63204 / 0.32 (13533) hydrogen bonds : bond 0.08548 / 5.48 ( 608) hydrogen bonds : angle 3.85806 / 2.81 ( 1806) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.332 Fit side-chains REVERT: A 65 ASP cc_start: 0.7619 (p0) cc_final: 0.7114 (m-30) REVERT: A 196 ASN cc_start: 0.7542 (OUTLIER) cc_final: 0.7111 (m110) REVERT: A 274 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7416 (mtp180) REVERT: A 556 TYR cc_start: 0.7239 (m-80) cc_final: 0.6644 (m-80) REVERT: A 744 MET cc_start: 0.7169 (tmm) cc_final: 0.6860 (ttm) REVERT: A 803 GLU cc_start: 0.7966 (tp30) cc_final: 0.7348 (mp0) REVERT: A 904 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6561 (tp) REVERT: A 936 GLU cc_start: 0.7794 (tt0) cc_final: 0.7157 (tt0) REVERT: A 958 MET cc_start: 0.8500 (tpt) cc_final: 0.8061 (ttp) REVERT: A 972 LYS cc_start: 0.8485 (mttt) cc_final: 0.8129 (mttp) REVERT: A 1131 MET cc_start: 0.4993 (tpt) cc_final: 0.4707 (mmp) REVERT: A 1181 GLN cc_start: 0.3266 (OUTLIER) cc_final: 0.2865 (pp30) REVERT: A 1197 ILE cc_start: 0.6022 (mp) cc_final: 0.5805 (mp) REVERT: A 1212 ASP cc_start: 0.8354 (m-30) cc_final: 0.7915 (m-30) outliers start: 25 outliers final: 11 residues processed: 85 average time/residue: 0.5597 time to fit residues: 51.4970 Evaluate side-chains 79 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1181 GLN Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 213 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.227601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.158846 restraints weight = 11241.107| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 3.14 r_work: 0.3754 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.7238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9987 Z= 0.143 Angle : 0.569 10.953 13533 Z= 0.283 Chirality : 0.040 0.170 1573 Planarity : 0.003 0.048 1682 Dihedral : 3.953 35.099 1351 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.41 % Allowed : 21.97 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.46 (0.24), residues: 1218 helix: 2.00 (0.19), residues: 790 sheet: 0.26 (0.79), residues: 47 loop : -1.19 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 385 TYR 0.014 0.001 TYR A 155 PHE 0.016 0.001 PHE A 336 TRP 0.023 0.002 TRP A 947 HIS 0.004 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 9987) covalent geometry : angle 0.56946 / 0.28 (13533) hydrogen bonds : bond 0.07324 / 4.68 ( 608) hydrogen bonds : angle 3.71862 / 2.72 ( 1806) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 65 ASP cc_start: 0.7627 (p0) cc_final: 0.7091 (m-30) REVERT: A 196 ASN cc_start: 0.7362 (OUTLIER) cc_final: 0.7044 (m110) REVERT: A 274 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7368 (mtp180) REVERT: A 556 TYR cc_start: 0.7140 (m-80) cc_final: 0.6575 (m-80) REVERT: A 744 MET cc_start: 0.7102 (tmm) cc_final: 0.6821 (ttm) REVERT: A 803 GLU cc_start: 0.7883 (tp30) cc_final: 0.7245 (mp0) REVERT: A 904 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6460 (tp) REVERT: A 936 GLU cc_start: 0.7438 (tt0) cc_final: 0.7105 (tt0) REVERT: A 958 MET cc_start: 0.8504 (tpt) cc_final: 0.8036 (ttp) REVERT: A 972 LYS cc_start: 0.8453 (mttt) cc_final: 0.8097 (mttp) REVERT: A 1047 ASN cc_start: 0.4406 (m-40) cc_final: 0.3415 (m-40) REVERT: A 1131 MET cc_start: 0.4939 (tpt) cc_final: 0.4712 (mmp) REVERT: A 1157 GLU cc_start: 0.6698 (mp0) cc_final: 0.5861 (tm-30) REVERT: A 1181 GLN cc_start: 0.3176 (OUTLIER) cc_final: 0.2799 (pp30) REVERT: A 1197 ILE cc_start: 0.6000 (mp) cc_final: 0.5790 (mp) REVERT: A 1212 ASP cc_start: 0.8451 (m-30) cc_final: 0.7979 (m-30) outliers start: 15 outliers final: 9 residues processed: 83 average time/residue: 0.5827 time to fit residues: 52.1193 Evaluate side-chains 82 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1181 GLN Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 GLN ** 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 = 0.4638 r_free = 0.4638 target = 0.227475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.159267 restraints weight = 11301.580| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 3.18 r_work: 0.3748 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.7243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 9987 Z= 0.217 Angle : 0.869 59.174 13533 Z= 0.505 Chirality : 0.041 0.250 1573 Planarity : 0.003 0.048 1682 Dihedral : 3.953 35.099 1351 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.31 % Allowed : 22.25 % Favored : 76.43 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.63 % 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: 1.46 (0.24), residues: 1218 helix: 2.00 (0.19), residues: 790 sheet: 0.27 (0.79), residues: 47 loop : -1.20 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1189 TYR 0.013 0.001 TYR A 155 PHE 0.015 0.001 PHE A 336 TRP 0.023 0.002 TRP A 947 HIS 0.004 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.22 ( 9987) covalent geometry : angle 0.86949 / 0.50 (13533) hydrogen bonds : bond 0.07313 / 4.67 ( 608) hydrogen bonds : angle 3.72027 / 2.72 ( 1806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3852.90 seconds wall clock time: 66 minutes 17.93 seconds (3977.93 seconds total)