Starting phenix.real_space_refine on Thu Aug 6 04:45:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kor_62479/08_2026/9kor_62479.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kor_62479/08_2026/9kor_62479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kor_62479/08_2026/9kor_62479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kor_62479/08_2026/9kor_62479.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kor_62479/08_2026/9kor_62479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kor_62479/08_2026/9kor_62479.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 150 5.49 5 Mg 4 5.21 5 S 32 5.16 5 C 7778 2.51 5 N 2326 2.21 5 O 2886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 13176 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1229, 10004 Classifications: {'peptide': 1229} Link IDs: {'PTRANS': 36, 'TRANS': 1192} Chain breaks: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2584 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 10, 'rna3p_pur': 53, 'rna3p_pyr': 44} Link IDs: {'rna2p': 24, 'rna3p': 96} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "D" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 500 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.18, per 1000 atoms: 0.24 Number of scatterers: 13176 At special positions: 0 Unit cell: (91.14, 112.53, 145.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 150 15.00 Mg 4 11.99 O 2886 8.00 N 2326 7.00 C 7778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 617.9 milliseconds 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 53.1% alpha, 12.2% beta 42 base pairs and 91 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 50 through 82 Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 110 through 117 removed outlier: 3.769A pdb=" N VAL A 113 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 117 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 removed outlier: 3.670A pdb=" N PHE A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N CYS A 124 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 148 Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 167 through 177 removed outlier: 3.781A pdb=" N GLN A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 203 Processing helix chain 'A' and resid 208 through 223 Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 235 through 248 Processing helix chain 'A' and resid 250 through 256 Processing helix chain 'A' and resid 260 through 266 removed outlier: 3.879A pdb=" N LYS A 264 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASN A 265 " --> pdb=" O SER A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 280 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.911A pdb=" N ILE A 320 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 350 through 362 removed outlier: 3.529A pdb=" N ILE A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 397 through 412 Processing helix chain 'A' and resid 433 through 443 Processing helix chain 'A' and resid 451 through 471 Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.551A pdb=" N VAL A 477 " --> pdb=" O TRP A 474 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU A 478 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 501 removed outlier: 3.809A pdb=" N ARG A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 521 through 525 removed outlier: 4.043A pdb=" N SER A 524 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 541 Processing helix chain 'A' and resid 543 through 558 Processing helix chain 'A' and resid 564 through 587 Processing helix chain 'A' and resid 589 through 595 removed outlier: 3.748A pdb=" N LYS A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 611 removed outlier: 3.568A pdb=" N LEU A 602 " --> pdb=" O ASN A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 632 Processing helix chain 'A' and resid 652 through 675 removed outlier: 4.584A pdb=" N LEU A 668 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 675 " --> pdb=" O GLU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 901 removed outlier: 3.530A pdb=" N TRP A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLU A 895 " --> pdb=" O GLU A 891 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TRP A 896 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 900 " --> pdb=" O TRP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 919 removed outlier: 3.726A pdb=" N ASP A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 940 through 954 removed outlier: 4.076A pdb=" N HIS A 944 " --> pdb=" O PRO A 940 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA A 945 " --> pdb=" O ILE A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 979 Processing helix chain 'A' and resid 1003 through 1007 Processing helix chain 'A' and resid 1045 through 1054 removed outlier: 4.080A pdb=" N LEU A1049 " --> pdb=" O ASP A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1088 Processing helix chain 'A' and resid 1091 through 1104 Processing helix chain 'A' and resid 1126 through 1131 Processing helix chain 'A' and resid 1132 through 1135 Processing helix chain 'A' and resid 1143 through 1147 removed outlier: 3.605A pdb=" N GLY A1147 " --> pdb=" O ASN A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1166 removed outlier: 3.663A pdb=" N GLU A1160 " --> pdb=" O PRO A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1198 Processing helix chain 'A' and resid 1269 through 1272 Processing helix chain 'A' and resid 1325 through 1332 Processing helix chain 'A' and resid 1338 through 1342 Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.807A pdb=" N GLN A1361 " --> pdb=" O VAL A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1370 No H-bonds generated for 'chain 'A' and resid 1368 through 1370' Processing helix chain 'A' and resid 1392 through 1410 Processing sheet with id=AA1, first strand: chain 'A' and resid 904 through 910 removed outlier: 6.040A pdb=" N ASP A 684 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ASP A 907 " --> pdb=" O ASP A 684 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A 686 " --> pdb=" O ASP A 907 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N TYR A 909 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU A 688 " --> pdb=" O TYR A 909 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA A 35 " --> pdb=" O ASN A 989 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE A 991 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A 37 " --> pdb=" O ILE A 991 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ILE A1376 " --> pdb=" O LEU A 990 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLN A1372 " --> pdb=" O CYS A1387 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N CYS A1387 " --> pdb=" O GLN A1372 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS A1383 " --> pdb=" O ILE A1376 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU A1378 " --> pdb=" O THR A1381 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N THR A1381 " --> pdb=" O LEU A1378 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 904 through 910 removed outlier: 6.040A pdb=" N ASP A 684 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ASP A 907 " --> pdb=" O ASP A 684 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A 686 " --> pdb=" O ASP A 907 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N TYR A 909 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU A 688 " --> pdb=" O TYR A 909 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA A 35 " --> pdb=" O ASN A 989 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE A 991 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A 37 " --> pdb=" O ILE A 991 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ILE A1376 " --> pdb=" O LEU A 990 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA4, first strand: chain 'A' and resid 1215 through 1218 removed outlier: 6.247A pdb=" N ASN A1110 " --> pdb=" O ILE A1014 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ILE A1014 " --> pdb=" O ASN A1110 " (cutoff:3.500A) removed outlier: 13.699A pdb=" N SER A1112 " --> pdb=" O GLU A1012 " (cutoff:3.500A) removed outlier: 18.546A pdb=" N GLU A1012 " --> pdb=" O SER A1112 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET A1243 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY A1013 " --> pdb=" O LEU A1241 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A1241 " --> pdb=" O GLY A1013 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N PHE A1015 " --> pdb=" O TYR A1239 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N TYR A1239 " --> pdb=" O PHE A1015 " (cutoff:3.500A) removed outlier: 12.817A pdb=" N GLU A1017 " --> pdb=" O ASP A1237 " (cutoff:3.500A) removed outlier: 14.857A pdb=" N ASP A1237 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1040 through 1043 removed outlier: 4.240A pdb=" N CYS A1029 " --> pdb=" O VAL A1043 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1117 through 1118 Processing sheet with id=AA7, first strand: chain 'A' and resid 1137 through 1141 Processing sheet with id=AA8, first strand: chain 'A' and resid 1266 through 1267 removed outlier: 7.850A pdb=" N LEU A1266 " --> pdb=" O LYS A1250 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 91 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2157 1.33 - 1.45: 4248 1.45 - 1.57: 6980 1.57 - 1.69: 298 1.69 - 1.81: 50 Bond restraints: 13733 Sorted by residual: bond pdb=" C1' DC D 13 " pdb=" N1 DC D 13 " ideal model delta sigma weight residual 1.468 1.528 -0.060 1.40e-02 5.10e+03 1.81e+01 bond pdb=" C3' DC D 25 " pdb=" C2' DC D 25 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C1' DC D 20 " pdb=" N1 DC D 20 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C1' DC D 11 " pdb=" N1 DC D 11 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.71e+00 bond pdb=" C2 DC D 21 " pdb=" O2 DC D 21 " ideal model delta sigma weight residual 1.240 1.212 0.028 9.00e-03 1.23e+04 9.49e+00 ... (remaining 13728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 18812 2.31 - 4.63: 395 4.63 - 6.94: 32 6.94 - 9.26: 1 9.26 - 11.57: 2 Bond angle restraints: 19242 Sorted by residual: angle pdb=" O4' A B 32 " pdb=" C1' A B 32 " pdb=" N9 A B 32 " ideal model delta sigma weight residual 108.20 113.77 -5.57 8.00e-01 1.56e+00 4.85e+01 angle pdb=" O4' A B 42 " pdb=" C1' A B 42 " pdb=" N9 A B 42 " ideal model delta sigma weight residual 108.20 113.07 -4.87 8.00e-01 1.56e+00 3.70e+01 angle pdb=" C1' U B 25 " pdb=" N1 U B 25 " pdb=" C2 U B 25 " ideal model delta sigma weight residual 117.70 124.32 -6.62 1.20e+00 6.94e-01 3.05e+01 angle pdb=" C1' C B 55 " pdb=" N1 C B 55 " pdb=" C2 C B 55 " ideal model delta sigma weight residual 118.80 124.87 -6.07 1.10e+00 8.26e-01 3.05e+01 angle pdb=" O2 U B 25 " pdb=" C2 U B 25 " pdb=" N3 U B 25 " ideal model delta sigma weight residual 122.20 118.35 3.85 7.00e-01 2.04e+00 3.03e+01 ... (remaining 19237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 7844 35.99 - 71.97: 478 71.97 - 107.96: 49 107.96 - 143.94: 1 143.94 - 179.93: 17 Dihedral angle restraints: 8389 sinusoidal: 4766 harmonic: 3623 Sorted by residual: dihedral pdb=" O4' U B 64 " pdb=" C1' U B 64 " pdb=" N1 U B 64 " pdb=" C2 U B 64 " ideal model delta sinusoidal sigma weight residual -160.00 19.93 -179.93 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U B 26 " pdb=" C1' U B 26 " pdb=" N1 U B 26 " pdb=" C2 U B 26 " ideal model delta sinusoidal sigma weight residual 200.00 21.31 178.69 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C B 17 " pdb=" C1' C B 17 " pdb=" N1 C B 17 " pdb=" C2 C B 17 " ideal model delta sinusoidal sigma weight residual 200.00 23.45 176.55 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 8386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2045 0.093 - 0.187: 185 0.187 - 0.280: 6 0.280 - 0.374: 0 0.374 - 0.467: 1 Chirality restraints: 2237 Sorted by residual: chirality pdb=" C1' A B 32 " pdb=" O4' A B 32 " pdb=" C2' A B 32 " pdb=" N9 A B 32 " both_signs ideal model delta sigma weight residual False 2.44 1.97 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" C1' A B 42 " pdb=" O4' A B 42 " pdb=" C2' A B 42 " pdb=" N9 A B 42 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.26 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CG LEU A 513 " pdb=" CB LEU A 513 " pdb=" CD1 LEU A 513 " pdb=" CD2 LEU A 513 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 2234 not shown) Planarity restraints: 1913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 27 " -0.079 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO A 28 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO A 28 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 28 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC D 21 " 0.007 2.00e-02 2.50e+03 2.81e-02 1.78e+01 pdb=" N1 DC D 21 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DC D 21 " -0.071 2.00e-02 2.50e+03 pdb=" O2 DC D 21 " 0.043 2.00e-02 2.50e+03 pdb=" N3 DC D 21 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC D 21 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC D 21 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC D 21 " 0.011 2.00e-02 2.50e+03 pdb=" C6 DC D 21 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 32 " 0.048 2.00e-02 2.50e+03 2.33e-02 1.49e+01 pdb=" N9 A B 32 " -0.059 2.00e-02 2.50e+03 pdb=" C8 A B 32 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A B 32 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A B 32 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A B 32 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A B 32 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A B 32 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A B 32 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A B 32 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A B 32 " -0.001 2.00e-02 2.50e+03 ... (remaining 1910 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 444 2.67 - 3.23: 12515 3.23 - 3.79: 22957 3.79 - 4.34: 31004 4.34 - 4.90: 47206 Nonbonded interactions: 114126 Sorted by model distance: nonbonded pdb=" NH2 ARG A 100 " pdb=" OP1 G B 19 " model vdw 2.119 3.120 nonbonded pdb=" O LEU A 411 " pdb=" OH TYR A 463 " model vdw 2.130 3.040 nonbonded pdb=" OE1 GLN A1294 " pdb=" OH TYR A1296 " model vdw 2.205 3.040 nonbonded pdb=" NZ LYS A 492 " pdb=" OP1 C B 8 " model vdw 2.211 3.120 nonbonded pdb=" OG SER A 618 " pdb=" OP2 C B 7 " model vdw 2.215 3.040 ... (remaining 114121 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.670 Find NCS groups from input model: 0.060 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:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 : 0.003 0.093 13733 Z= 0.243 Angle : 0.699 11.573 19242 Z= 0.561 Chirality : 0.050 0.467 2237 Planarity : 0.005 0.119 1913 Dihedral : 21.623 179.928 6039 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.29 % Favored : 93.39 % Rotamer: Outliers : 0.91 % Allowed : 16.30 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.25), residues: 1225 helix: 0.99 (0.22), residues: 571 sheet: 0.37 (0.48), residues: 128 loop : -1.00 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 104 TYR 0.024 0.001 TYR A1194 PHE 0.017 0.001 PHE A1356 TRP 0.029 0.002 TRP A 338 HIS 0.003 0.001 HIS A1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.24 (13733) covalent geometry : angle 0.69925 / 0.56 (19242) hydrogen bonds : bond 0.13747 / 8.95 ( 582) hydrogen bonds : angle 5.64170 / 4.05 ( 1556) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 15 TYR cc_start: 0.7875 (m-10) cc_final: 0.7671 (m-10) REVERT: A 292 GLN cc_start: 0.7609 (tm-30) cc_final: 0.6959 (tp40) REVERT: A 461 GLN cc_start: 0.6632 (mm-40) cc_final: 0.6136 (mt0) REVERT: A 467 ASP cc_start: 0.7031 (t0) cc_final: 0.6788 (t70) REVERT: A 482 MET cc_start: 0.8343 (mtp) cc_final: 0.8136 (mtp) REVERT: A 486 ASP cc_start: 0.7967 (m-30) cc_final: 0.7638 (t0) REVERT: A 987 GLU cc_start: 0.6174 (pt0) cc_final: 0.5853 (tp30) REVERT: A 994 LYS cc_start: 0.7840 (pttm) cc_final: 0.7438 (ptmm) REVERT: A 1044 LYS cc_start: 0.7554 (ptpt) cc_final: 0.7267 (pttt) REVERT: A 1121 ASN cc_start: 0.7638 (t0) cc_final: 0.7191 (t0) REVERT: A 1122 ARG cc_start: 0.7337 (mmm160) cc_final: 0.6400 (mtp180) REVERT: A 1186 THR cc_start: 0.6104 (m) cc_final: 0.5878 (m) REVERT: A 1246 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7311 (t0) REVERT: A 1257 LYS cc_start: 0.7974 (mmmt) cc_final: 0.7206 (mtmt) REVERT: A 1285 LYS cc_start: 0.7836 (ptpt) cc_final: 0.7498 (mmmt) REVERT: A 1347 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7072 (tppt) outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 0.5584 time to fit residues: 56.2811 Evaluate side-chains 89 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 1245 ASN Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1347 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.0030 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN A1294 GLN A1406 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.235455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.190565 restraints weight = 13451.159| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 1.64 r_work: 0.4041 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3925 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 13733 Z= 0.242 Angle : 0.667 7.523 19242 Z= 0.375 Chirality : 0.047 0.341 2237 Planarity : 0.006 0.120 1913 Dihedral : 23.222 179.538 3518 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.96 % Favored : 93.71 % Rotamer: Outliers : 3.62 % Allowed : 14.31 % Favored : 82.07 % 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: 0.09 (0.24), residues: 1225 helix: 1.01 (0.22), residues: 570 sheet: 0.31 (0.49), residues: 108 loop : -1.00 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1159 TYR 0.014 0.002 TYR A1386 PHE 0.019 0.002 PHE A 66 TRP 0.018 0.002 TRP A 338 HIS 0.009 0.002 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.24 (13733) covalent geometry : angle 0.66683 / 0.38 (19242) hydrogen bonds : bond 0.06035 / 4.02 ( 582) hydrogen bonds : angle 4.65992 / 3.35 ( 1556) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 84 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 288 LYS cc_start: 0.7688 (tmtm) cc_final: 0.7192 (mmtt) REVERT: A 292 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7052 (tp40) REVERT: A 308 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7607 (mt) REVERT: A 381 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7222 (mtt-85) REVERT: A 461 GLN cc_start: 0.6838 (mm-40) cc_final: 0.6344 (tp-100) REVERT: A 467 ASP cc_start: 0.7292 (t0) cc_final: 0.7021 (t70) REVERT: A 482 MET cc_start: 0.8430 (mtp) cc_final: 0.8142 (mtm) REVERT: A 483 GLU cc_start: 0.7903 (tt0) cc_final: 0.7663 (pt0) REVERT: A 655 ARG cc_start: 0.7258 (ttt-90) cc_final: 0.5831 (ttp-110) REVERT: A 984 MET cc_start: 0.4525 (mpp) cc_final: 0.4215 (mpp) REVERT: A 987 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5771 (tp30) REVERT: A 994 LYS cc_start: 0.8028 (pttm) cc_final: 0.7587 (ptmm) REVERT: A 1010 MET cc_start: 0.7875 (mpt) cc_final: 0.7645 (mpt) REVERT: A 1044 LYS cc_start: 0.7776 (ptpt) cc_final: 0.7384 (pttt) REVERT: A 1121 ASN cc_start: 0.7774 (t0) cc_final: 0.7295 (t0) REVERT: A 1122 ARG cc_start: 0.7367 (mmm160) cc_final: 0.6530 (mtp180) REVERT: A 1186 THR cc_start: 0.6367 (OUTLIER) cc_final: 0.6105 (m) REVERT: A 1195 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6747 (m-30) REVERT: A 1257 LYS cc_start: 0.8046 (mmmt) cc_final: 0.7308 (mtmt) REVERT: A 1285 LYS cc_start: 0.7928 (ptpt) cc_final: 0.7546 (mmmt) REVERT: A 1347 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7264 (tppt) outliers start: 40 outliers final: 12 residues processed: 117 average time/residue: 0.5647 time to fit residues: 72.8706 Evaluate side-chains 99 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1245 ASN Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1347 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 30.0000 chunk 80 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 95 optimal weight: 0.2980 chunk 26 optimal weight: 0.1980 chunk 131 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.236076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.191549 restraints weight = 13583.068| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 1.63 r_work: 0.4063 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 13733 Z= 0.194 Angle : 0.600 7.020 19242 Z= 0.346 Chirality : 0.044 0.349 2237 Planarity : 0.005 0.120 1913 Dihedral : 23.250 179.348 3514 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.22 % Favored : 94.37 % Rotamer: Outliers : 3.44 % Allowed : 14.95 % Favored : 81.61 % 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: 0.16 (0.24), residues: 1225 helix: 1.10 (0.22), residues: 570 sheet: 0.45 (0.49), residues: 111 loop : -1.03 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1211 TYR 0.015 0.002 TYR A1194 PHE 0.018 0.002 PHE A 242 TRP 0.015 0.002 TRP A 355 HIS 0.006 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (13733) covalent geometry : angle 0.59982 / 0.35 (19242) hydrogen bonds : bond 0.05783 / 3.86 ( 582) hydrogen bonds : angle 4.53082 / 3.25 ( 1556) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 88 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.8788 (mmp) cc_final: 0.8408 (mmm) REVERT: A 288 LYS cc_start: 0.7624 (tmtm) cc_final: 0.7069 (mmtt) REVERT: A 292 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7021 (tp40) REVERT: A 368 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7600 (tt) REVERT: A 381 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7597 (mtt-85) REVERT: A 461 GLN cc_start: 0.6769 (mm-40) cc_final: 0.6265 (tp-100) REVERT: A 467 ASP cc_start: 0.7325 (t0) cc_final: 0.7032 (t70) REVERT: A 482 MET cc_start: 0.8339 (mtp) cc_final: 0.8070 (mtm) REVERT: A 483 GLU cc_start: 0.7884 (tt0) cc_final: 0.7315 (pt0) REVERT: A 655 ARG cc_start: 0.7234 (ttt-90) cc_final: 0.5731 (ttp-110) REVERT: A 987 GLU cc_start: 0.6192 (OUTLIER) cc_final: 0.5628 (tp30) REVERT: A 994 LYS cc_start: 0.8031 (pttm) cc_final: 0.7561 (ptmm) REVERT: A 1044 LYS cc_start: 0.7764 (ptpt) cc_final: 0.7334 (pttt) REVERT: A 1121 ASN cc_start: 0.7766 (t0) cc_final: 0.7260 (t0) REVERT: A 1122 ARG cc_start: 0.7334 (mmm160) cc_final: 0.6592 (mmm-85) REVERT: A 1186 THR cc_start: 0.6452 (OUTLIER) cc_final: 0.5961 (m) REVERT: A 1257 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7286 (mtmt) REVERT: A 1285 LYS cc_start: 0.7897 (ptpt) cc_final: 0.7474 (tptm) REVERT: A 1347 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7160 (tppt) outliers start: 38 outliers final: 10 residues processed: 116 average time/residue: 0.5603 time to fit residues: 71.8205 Evaluate side-chains 94 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1245 ASN Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1347 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 113 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 125 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 ASN A 607 ASN A1323 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.235350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.191060 restraints weight = 13470.082| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 1.64 r_work: 0.4046 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3930 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 13733 Z= 0.194 Angle : 0.600 6.950 19242 Z= 0.344 Chirality : 0.044 0.350 2237 Planarity : 0.005 0.120 1913 Dihedral : 23.294 178.854 3512 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.12 % Favored : 93.55 % Rotamer: Outliers : 4.26 % Allowed : 15.31 % Favored : 80.43 % 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: 0.14 (0.24), residues: 1225 helix: 1.16 (0.22), residues: 563 sheet: 0.39 (0.48), residues: 111 loop : -1.09 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1211 TYR 0.016 0.002 TYR A1194 PHE 0.019 0.002 PHE A 242 TRP 0.014 0.002 TRP A 355 HIS 0.006 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (13733) covalent geometry : angle 0.59998 / 0.34 (19242) hydrogen bonds : bond 0.05697 / 3.82 ( 582) hydrogen bonds : angle 4.48870 / 3.22 ( 1556) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 83 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.8817 (mmp) cc_final: 0.8331 (mmm) REVERT: A 288 LYS cc_start: 0.7629 (tmtm) cc_final: 0.7103 (mmtt) REVERT: A 292 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7036 (tp40) REVERT: A 376 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7606 (mp) REVERT: A 451 HIS cc_start: 0.3653 (OUTLIER) cc_final: 0.0505 (m-70) REVERT: A 461 GLN cc_start: 0.6760 (mm-40) cc_final: 0.6234 (tp-100) REVERT: A 467 ASP cc_start: 0.7365 (t0) cc_final: 0.7113 (t70) REVERT: A 482 MET cc_start: 0.8398 (mtp) cc_final: 0.8114 (mtm) REVERT: A 483 GLU cc_start: 0.7882 (tt0) cc_final: 0.7576 (pt0) REVERT: A 655 ARG cc_start: 0.7198 (ttt-90) cc_final: 0.5754 (ttp-110) REVERT: A 900 ASN cc_start: 0.5234 (OUTLIER) cc_final: 0.4581 (p0) REVERT: A 987 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5675 (tp30) REVERT: A 994 LYS cc_start: 0.8074 (pttm) cc_final: 0.7627 (ptmm) REVERT: A 1010 MET cc_start: 0.7897 (mpt) cc_final: 0.7672 (mpt) REVERT: A 1044 LYS cc_start: 0.7821 (ptpt) cc_final: 0.7386 (pttt) REVERT: A 1121 ASN cc_start: 0.7793 (t0) cc_final: 0.7225 (t0) REVERT: A 1122 ARG cc_start: 0.7328 (mmm160) cc_final: 0.6464 (mtp180) REVERT: A 1186 THR cc_start: 0.6404 (OUTLIER) cc_final: 0.6165 (m) REVERT: A 1257 LYS cc_start: 0.8048 (mmmt) cc_final: 0.7319 (mtmt) REVERT: A 1285 LYS cc_start: 0.7959 (ptpt) cc_final: 0.7524 (tptm) REVERT: A 1347 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7342 (tppt) outliers start: 47 outliers final: 21 residues processed: 119 average time/residue: 0.5395 time to fit residues: 71.1351 Evaluate side-chains 108 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1176 ASP Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1245 ASN Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1347 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 119 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 133 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 63 optimal weight: 0.0050 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.238138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.194234 restraints weight = 13543.293| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 1.58 r_work: 0.4086 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3972 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 13733 Z= 0.145 Angle : 0.556 6.316 19242 Z= 0.325 Chirality : 0.041 0.347 2237 Planarity : 0.005 0.120 1913 Dihedral : 23.282 179.585 3512 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.22 % Favored : 94.45 % Rotamer: Outliers : 4.26 % Allowed : 16.03 % Favored : 79.71 % 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: 0.32 (0.24), residues: 1225 helix: 1.31 (0.22), residues: 564 sheet: 0.58 (0.50), residues: 105 loop : -1.02 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 381 TYR 0.013 0.001 TYR A 48 PHE 0.018 0.001 PHE A 242 TRP 0.014 0.002 TRP A 355 HIS 0.004 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (13733) covalent geometry : angle 0.55580 / 0.32 (19242) hydrogen bonds : bond 0.05376 / 3.60 ( 582) hydrogen bonds : angle 4.35218 / 3.12 ( 1556) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 89 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 288 LYS cc_start: 0.7533 (tmtm) cc_final: 0.7096 (mmtt) REVERT: A 292 GLN cc_start: 0.7746 (tm-30) cc_final: 0.6994 (tp40) REVERT: A 461 GLN cc_start: 0.6715 (mm-40) cc_final: 0.6213 (tp-100) REVERT: A 467 ASP cc_start: 0.7294 (t0) cc_final: 0.7019 (t70) REVERT: A 482 MET cc_start: 0.8243 (mtp) cc_final: 0.7983 (mtm) REVERT: A 655 ARG cc_start: 0.7176 (ttt-90) cc_final: 0.5678 (ttp-110) REVERT: A 660 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7078 (mmm-85) REVERT: A 984 MET cc_start: 0.4523 (mpp) cc_final: 0.4147 (mpp) REVERT: A 987 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5546 (tp30) REVERT: A 994 LYS cc_start: 0.8016 (pttm) cc_final: 0.7384 (ptmm) REVERT: A 1044 LYS cc_start: 0.7739 (ptpt) cc_final: 0.7324 (pttt) REVERT: A 1121 ASN cc_start: 0.7784 (t0) cc_final: 0.7193 (t0) REVERT: A 1122 ARG cc_start: 0.7279 (mmm160) cc_final: 0.6437 (mtp180) REVERT: A 1186 THR cc_start: 0.6382 (OUTLIER) cc_final: 0.5998 (m) REVERT: A 1257 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7317 (mtmt) REVERT: A 1285 LYS cc_start: 0.7888 (ptpt) cc_final: 0.7494 (tptm) REVERT: A 1288 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.5448 (tm-30) REVERT: A 1308 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7416 (mtpp) REVERT: A 1347 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7179 (tppt) outliers start: 47 outliers final: 20 residues processed: 125 average time/residue: 0.5683 time to fit residues: 78.3644 Evaluate side-chains 111 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1245 ASN Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1288 GLN Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1308 LYS Chi-restraints excluded: chain A residue 1347 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 ASN A 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.236658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.192977 restraints weight = 13422.141| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 1.62 r_work: 0.4060 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 13733 Z= 0.171 Angle : 0.574 6.389 19242 Z= 0.332 Chirality : 0.042 0.352 2237 Planarity : 0.005 0.120 1913 Dihedral : 23.297 179.519 3512 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.96 % Favored : 93.71 % Rotamer: Outliers : 4.26 % Allowed : 16.21 % Favored : 79.53 % 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: 0.28 (0.24), residues: 1225 helix: 1.33 (0.22), residues: 562 sheet: 0.63 (0.49), residues: 107 loop : -1.13 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 890 TYR 0.016 0.002 TYR A1194 PHE 0.019 0.001 PHE A 242 TRP 0.015 0.002 TRP A 355 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (13733) covalent geometry : angle 0.57439 / 0.33 (19242) hydrogen bonds : bond 0.05450 / 3.65 ( 582) hydrogen bonds : angle 4.34524 / 3.12 ( 1556) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 85 time to evaluate : 0.437 Fit side-chains REVERT: A 11 MET cc_start: 0.7344 (mmm) cc_final: 0.6552 (mtp) REVERT: A 50 MET cc_start: 0.8730 (mmp) cc_final: 0.8393 (mmm) REVERT: A 288 LYS cc_start: 0.7556 (tmtm) cc_final: 0.7062 (mtmm) REVERT: A 292 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7016 (tp40) REVERT: A 451 HIS cc_start: 0.3664 (OUTLIER) cc_final: 0.0505 (m-70) REVERT: A 457 ASP cc_start: 0.5709 (OUTLIER) cc_final: 0.5426 (t0) REVERT: A 461 GLN cc_start: 0.6753 (mm-40) cc_final: 0.6265 (tp-100) REVERT: A 467 ASP cc_start: 0.7336 (t0) cc_final: 0.7027 (t70) REVERT: A 482 MET cc_start: 0.8289 (mtp) cc_final: 0.8037 (mtm) REVERT: A 491 MET cc_start: 0.7031 (ptm) cc_final: 0.6819 (ptm) REVERT: A 655 ARG cc_start: 0.7139 (ttt-90) cc_final: 0.5685 (ttp-110) REVERT: A 660 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7053 (mmm-85) REVERT: A 668 LEU cc_start: 0.7851 (mt) cc_final: 0.7218 (pp) REVERT: A 984 MET cc_start: 0.4501 (mpp) cc_final: 0.4110 (mpp) REVERT: A 987 GLU cc_start: 0.6075 (OUTLIER) cc_final: 0.5541 (tp30) REVERT: A 994 LYS cc_start: 0.8085 (pttm) cc_final: 0.7454 (ptmm) REVERT: A 1044 LYS cc_start: 0.7807 (ptpt) cc_final: 0.7370 (pttt) REVERT: A 1045 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7404 (t0) REVERT: A 1121 ASN cc_start: 0.7837 (t0) cc_final: 0.7261 (t0) REVERT: A 1122 ARG cc_start: 0.7330 (mmm160) cc_final: 0.6486 (mtp180) REVERT: A 1186 THR cc_start: 0.6449 (OUTLIER) cc_final: 0.6100 (m) REVERT: A 1257 LYS cc_start: 0.8074 (mmmt) cc_final: 0.7353 (mtmt) REVERT: A 1285 LYS cc_start: 0.7919 (ptpt) cc_final: 0.7501 (tptm) REVERT: A 1288 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.5461 (tm-30) REVERT: A 1308 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7458 (mtpp) REVERT: A 1347 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7353 (tppt) outliers start: 47 outliers final: 19 residues processed: 122 average time/residue: 0.5032 time to fit residues: 67.9549 Evaluate side-chains 109 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1245 ASN Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1288 GLN Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1308 LYS Chi-restraints excluded: chain A residue 1347 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 0.0970 chunk 119 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.236427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.193064 restraints weight = 13442.233| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 1.55 r_work: 0.4073 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3960 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 13733 Z= 0.173 Angle : 0.574 6.363 19242 Z= 0.332 Chirality : 0.042 0.350 2237 Planarity : 0.005 0.120 1913 Dihedral : 23.307 179.489 3512 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.47 % Favored : 94.20 % Rotamer: Outliers : 4.44 % Allowed : 16.49 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1225 helix: 1.32 (0.22), residues: 562 sheet: 0.59 (0.49), residues: 107 loop : -1.16 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 890 TYR 0.014 0.002 TYR A1194 PHE 0.020 0.002 PHE A1356 TRP 0.017 0.002 TRP A 355 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (13733) covalent geometry : angle 0.57387 / 0.33 (19242) hydrogen bonds : bond 0.05424 / 3.63 ( 582) hydrogen bonds : angle 4.33827 / 3.12 ( 1556) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 83 time to evaluate : 0.313 Fit side-chains REVERT: A 11 MET cc_start: 0.7313 (mmm) cc_final: 0.6519 (mtp) REVERT: A 50 MET cc_start: 0.8712 (mmp) cc_final: 0.8262 (mmm) REVERT: A 288 LYS cc_start: 0.7552 (tmtm) cc_final: 0.7039 (mtmm) REVERT: A 292 GLN cc_start: 0.7756 (tm-30) cc_final: 0.6992 (tp40) REVERT: A 317 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: A 384 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6925 (ttp-170) REVERT: A 451 HIS cc_start: 0.3692 (OUTLIER) cc_final: 0.0562 (m-70) REVERT: A 457 ASP cc_start: 0.5708 (OUTLIER) cc_final: 0.5475 (t0) REVERT: A 461 GLN cc_start: 0.6683 (mm-40) cc_final: 0.6215 (tp-100) REVERT: A 467 ASP cc_start: 0.7316 (t0) cc_final: 0.7014 (t70) REVERT: A 482 MET cc_start: 0.8284 (mtp) cc_final: 0.8042 (mtm) REVERT: A 491 MET cc_start: 0.7010 (ptm) cc_final: 0.6808 (ptm) REVERT: A 655 ARG cc_start: 0.7063 (ttt-90) cc_final: 0.5643 (ttp-110) REVERT: A 660 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7167 (mmm-85) REVERT: A 987 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5501 (tp30) REVERT: A 994 LYS cc_start: 0.8085 (pttm) cc_final: 0.7465 (ptmm) REVERT: A 1044 LYS cc_start: 0.7858 (ptpt) cc_final: 0.7401 (pttt) REVERT: A 1045 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7370 (t0) REVERT: A 1121 ASN cc_start: 0.7820 (t0) cc_final: 0.7217 (t0) REVERT: A 1122 ARG cc_start: 0.7341 (mmm160) cc_final: 0.6451 (mtp180) REVERT: A 1257 LYS cc_start: 0.8059 (mmmt) cc_final: 0.7313 (mtmt) REVERT: A 1285 LYS cc_start: 0.7914 (ptpt) cc_final: 0.7424 (tptm) REVERT: A 1288 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.5424 (tm-30) REVERT: A 1308 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7473 (mtpp) REVERT: A 1347 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7344 (tppt) outliers start: 49 outliers final: 20 residues processed: 123 average time/residue: 0.5252 time to fit residues: 71.3756 Evaluate side-chains 112 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 384 ARG Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1245 ASN Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1288 GLN Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1308 LYS Chi-restraints excluded: chain A residue 1347 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 29 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.235201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.190962 restraints weight = 13262.997| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 1.56 r_work: 0.4055 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 13733 Z= 0.189 Angle : 0.595 6.492 19242 Z= 0.340 Chirality : 0.043 0.352 2237 Planarity : 0.005 0.120 1913 Dihedral : 23.338 179.309 3512 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.20 % Favored : 93.47 % Rotamer: Outliers : 4.53 % Allowed : 17.12 % Favored : 78.35 % 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: 0.17 (0.24), residues: 1225 helix: 1.24 (0.22), residues: 563 sheet: 0.58 (0.49), residues: 107 loop : -1.18 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 890 TYR 0.015 0.002 TYR A1194 PHE 0.019 0.002 PHE A 242 TRP 0.023 0.002 TRP A 355 HIS 0.006 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (13733) covalent geometry : angle 0.59485 / 0.34 (19242) hydrogen bonds : bond 0.05544 / 3.71 ( 582) hydrogen bonds : angle 4.37842 / 3.14 ( 1556) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 80 time to evaluate : 0.435 Fit side-chains REVERT: A 11 MET cc_start: 0.7311 (mmm) cc_final: 0.6574 (mtp) REVERT: A 50 MET cc_start: 0.8747 (mmp) cc_final: 0.8350 (mmm) REVERT: A 288 LYS cc_start: 0.7562 (tmtm) cc_final: 0.7089 (mtmm) REVERT: A 292 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7019 (tp40) REVERT: A 317 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: A 384 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6944 (ttp-170) REVERT: A 451 HIS cc_start: 0.3633 (OUTLIER) cc_final: 0.0583 (m-70) REVERT: A 457 ASP cc_start: 0.5704 (OUTLIER) cc_final: 0.5457 (t0) REVERT: A 461 GLN cc_start: 0.6695 (mm-40) cc_final: 0.6218 (tp-100) REVERT: A 467 ASP cc_start: 0.7294 (t0) cc_final: 0.7031 (t70) REVERT: A 482 MET cc_start: 0.8300 (mtp) cc_final: 0.8047 (mtm) REVERT: A 491 MET cc_start: 0.7043 (ptm) cc_final: 0.6842 (ptm) REVERT: A 655 ARG cc_start: 0.7046 (ttt-90) cc_final: 0.5658 (ttp-110) REVERT: A 660 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7142 (mmm-85) REVERT: A 668 LEU cc_start: 0.7846 (mt) cc_final: 0.7299 (pp) REVERT: A 984 MET cc_start: 0.4442 (mpp) cc_final: 0.4157 (mpp) REVERT: A 987 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.5612 (tp30) REVERT: A 994 LYS cc_start: 0.8122 (pttm) cc_final: 0.7528 (ptmm) REVERT: A 1044 LYS cc_start: 0.7864 (ptpt) cc_final: 0.7396 (pttt) REVERT: A 1045 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7398 (t0) REVERT: A 1122 ARG cc_start: 0.7296 (mmm160) cc_final: 0.6434 (mtp180) REVERT: A 1257 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7329 (mtmt) REVERT: A 1285 LYS cc_start: 0.7916 (ptpt) cc_final: 0.7504 (tptm) REVERT: A 1288 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.5324 (tm-30) REVERT: A 1308 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7495 (mtpp) REVERT: A 1347 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7351 (tppt) outliers start: 50 outliers final: 23 residues processed: 121 average time/residue: 0.5435 time to fit residues: 72.7884 Evaluate side-chains 114 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 384 ARG Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1176 ASP Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1245 ASN Chi-restraints excluded: chain A residue 1256 GLU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1288 GLN Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1308 LYS Chi-restraints excluded: chain A residue 1347 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 133 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.236485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.193136 restraints weight = 13510.100| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 1.55 r_work: 0.4073 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 13733 Z= 0.167 Angle : 0.574 6.294 19242 Z= 0.332 Chirality : 0.042 0.348 2237 Planarity : 0.005 0.119 1913 Dihedral : 23.328 179.576 3512 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.55 % Favored : 94.12 % Rotamer: Outliers : 3.71 % Allowed : 18.21 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.24), residues: 1225 helix: 1.25 (0.22), residues: 563 sheet: 0.57 (0.49), residues: 107 loop : -1.15 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1211 TYR 0.015 0.002 TYR A1194 PHE 0.022 0.001 PHE A1356 TRP 0.015 0.002 TRP A 355 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (13733) covalent geometry : angle 0.57446 / 0.33 (19242) hydrogen bonds : bond 0.05438 / 3.64 ( 582) hydrogen bonds : angle 4.34234 / 3.12 ( 1556) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 84 time to evaluate : 0.440 Fit side-chains REVERT: A 11 MET cc_start: 0.7288 (mmm) cc_final: 0.6516 (mtp) REVERT: A 50 MET cc_start: 0.8714 (mmp) cc_final: 0.8297 (mmm) REVERT: A 288 LYS cc_start: 0.7512 (tmtm) cc_final: 0.7028 (mtmm) REVERT: A 292 GLN cc_start: 0.7762 (tm-30) cc_final: 0.6993 (tp40) REVERT: A 317 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: A 451 HIS cc_start: 0.3556 (OUTLIER) cc_final: 0.0514 (m-70) REVERT: A 457 ASP cc_start: 0.5592 (OUTLIER) cc_final: 0.5323 (t0) REVERT: A 461 GLN cc_start: 0.6675 (mm-40) cc_final: 0.6084 (tp-100) REVERT: A 467 ASP cc_start: 0.7266 (t0) cc_final: 0.7032 (t70) REVERT: A 482 MET cc_start: 0.8295 (mtp) cc_final: 0.8011 (mtm) REVERT: A 491 MET cc_start: 0.7006 (ptm) cc_final: 0.6796 (ptm) REVERT: A 655 ARG cc_start: 0.7075 (ttt-90) cc_final: 0.5635 (ttp-110) REVERT: A 660 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7192 (mmm-85) REVERT: A 668 LEU cc_start: 0.7775 (mt) cc_final: 0.7248 (pp) REVERT: A 984 MET cc_start: 0.4353 (mpp) cc_final: 0.4054 (mpp) REVERT: A 987 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.5558 (tp30) REVERT: A 994 LYS cc_start: 0.8107 (pttm) cc_final: 0.7472 (ptmm) REVERT: A 1044 LYS cc_start: 0.7861 (ptpt) cc_final: 0.7366 (pttt) REVERT: A 1045 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7408 (t0) REVERT: A 1121 ASN cc_start: 0.7615 (t0) cc_final: 0.7136 (t0) REVERT: A 1122 ARG cc_start: 0.7252 (mmm160) cc_final: 0.6486 (mmm-85) REVERT: A 1257 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7284 (mtmt) REVERT: A 1285 LYS cc_start: 0.7910 (ptpt) cc_final: 0.7495 (tptm) REVERT: A 1288 GLN cc_start: 0.6678 (OUTLIER) cc_final: 0.5379 (tm-30) REVERT: A 1308 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7494 (mtpp) REVERT: A 1347 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7351 (tppt) outliers start: 41 outliers final: 22 residues processed: 116 average time/residue: 0.5184 time to fit residues: 66.3092 Evaluate side-chains 112 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1245 ASN Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1256 GLU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1288 GLN Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1308 LYS Chi-restraints excluded: chain A residue 1347 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 65 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 99 optimal weight: 0.0770 chunk 69 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.237734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.194277 restraints weight = 13509.646| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 1.58 r_work: 0.4090 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3975 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 13733 Z= 0.142 Angle : 0.564 7.383 19242 Z= 0.327 Chirality : 0.042 0.347 2237 Planarity : 0.005 0.119 1913 Dihedral : 23.314 179.961 3512 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.04 % Favored : 93.71 % Rotamer: Outliers : 3.08 % Allowed : 18.75 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.29 (0.24), residues: 1225 helix: 1.29 (0.22), residues: 565 sheet: 0.77 (0.51), residues: 101 loop : -1.09 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1211 TYR 0.014 0.002 TYR A 48 PHE 0.023 0.001 PHE A1356 TRP 0.019 0.002 TRP A 516 HIS 0.003 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (13733) covalent geometry : angle 0.56376 / 0.33 (19242) hydrogen bonds : bond 0.05287 / 3.53 ( 582) hydrogen bonds : angle 4.28552 / 3.08 ( 1556) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.536 Fit side-chains REVERT: A 11 MET cc_start: 0.7293 (mmm) cc_final: 0.6521 (mtp) REVERT: A 50 MET cc_start: 0.8710 (mmp) cc_final: 0.8294 (mmm) REVERT: A 288 LYS cc_start: 0.7491 (tmtm) cc_final: 0.6996 (mtmm) REVERT: A 292 GLN cc_start: 0.7721 (tm-30) cc_final: 0.6972 (tp40) REVERT: A 457 ASP cc_start: 0.5570 (OUTLIER) cc_final: 0.5297 (t0) REVERT: A 461 GLN cc_start: 0.6669 (mm-40) cc_final: 0.6203 (tp-100) REVERT: A 467 ASP cc_start: 0.7249 (t0) cc_final: 0.6998 (t70) REVERT: A 482 MET cc_start: 0.8268 (mtp) cc_final: 0.8016 (mtm) REVERT: A 491 MET cc_start: 0.7002 (ptm) cc_final: 0.6759 (ptm) REVERT: A 655 ARG cc_start: 0.7062 (ttt-90) cc_final: 0.5646 (ttp-110) REVERT: A 660 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7123 (mmm-85) REVERT: A 668 LEU cc_start: 0.7767 (mt) cc_final: 0.7276 (pp) REVERT: A 890 ARG cc_start: 0.7156 (mpt-90) cc_final: 0.6750 (mpt-90) REVERT: A 984 MET cc_start: 0.4331 (mpp) cc_final: 0.4047 (mpp) REVERT: A 987 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5513 (tp30) REVERT: A 994 LYS cc_start: 0.8076 (pttm) cc_final: 0.7426 (ptmm) REVERT: A 1044 LYS cc_start: 0.7875 (ptpt) cc_final: 0.7368 (pttt) REVERT: A 1045 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7389 (t0) REVERT: A 1121 ASN cc_start: 0.7659 (t0) cc_final: 0.7144 (t0) REVERT: A 1122 ARG cc_start: 0.7281 (mmm160) cc_final: 0.6517 (mmm-85) REVERT: A 1257 LYS cc_start: 0.8022 (mmmt) cc_final: 0.7254 (mtmt) REVERT: A 1285 LYS cc_start: 0.7945 (ptpt) cc_final: 0.7500 (tptm) REVERT: A 1288 GLN cc_start: 0.6695 (OUTLIER) cc_final: 0.5411 (tm-30) REVERT: A 1308 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7469 (mtpp) REVERT: A 1347 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7198 (tppt) outliers start: 34 outliers final: 20 residues processed: 109 average time/residue: 0.5026 time to fit residues: 60.4889 Evaluate side-chains 109 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1045 ASP Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1245 ASN Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1256 GLU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1288 GLN Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1308 LYS Chi-restraints excluded: chain A residue 1347 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 3 optimal weight: 1.9990 chunk 109 optimal weight: 0.0980 chunk 16 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.236891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.193526 restraints weight = 13442.176| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 1.55 r_work: 0.4080 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3964 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 13733 Z= 0.161 Angle : 0.576 7.391 19242 Z= 0.331 Chirality : 0.042 0.350 2237 Planarity : 0.005 0.119 1913 Dihedral : 23.319 179.985 3512 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.88 % Favored : 93.88 % Rotamer: Outliers : 2.81 % Allowed : 19.02 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.24), residues: 1225 helix: 1.30 (0.22), residues: 563 sheet: 0.77 (0.50), residues: 101 loop : -1.13 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 890 TYR 0.015 0.002 TYR A1194 PHE 0.020 0.001 PHE A1356 TRP 0.020 0.002 TRP A 355 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (13733) covalent geometry : angle 0.57624 / 0.33 (19242) hydrogen bonds : bond 0.05338 / 3.57 ( 582) hydrogen bonds : angle 4.29771 / 3.09 ( 1556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4307.87 seconds wall clock time: 74 minutes 23.62 seconds (4463.62 seconds total)