Starting phenix.real_space_refine on Fri Jul 3 10:07:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kor_62479/07_2026/9kor_62479.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kor_62479/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9kor_62479/07_2026/9kor_62479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kor_62479/07_2026/9kor_62479.map" model { file = "/net/cci-nas-00/data/ceres_data/9kor_62479/07_2026/9kor_62479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kor_62479/07_2026/9kor_62479.cif" } 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-dev-6108/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: 2.25, per 1000 atoms: 0.17 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: 0.91 Conformation dependent library (CDL) restraints added in 408.7 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: 1.44 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: 3.08 Time building geometry restraints manager: 1.18 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: 18979 2.31 - 4.63: 229 4.63 - 6.94: 31 6.94 - 9.26: 1 9.26 - 11.57: 2 Bond angle restraints: 19242 Sorted by residual: 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 angle pdb=" N1 C B 107 " pdb=" C2 C B 107 " pdb=" O2 C B 107 " ideal model delta sigma weight residual 118.90 122.04 -3.14 6.00e-01 2.78e+00 2.75e+01 angle pdb=" C1' C B 107 " pdb=" N1 C B 107 " pdb=" C2 C B 107 " ideal model delta sigma weight residual 118.80 124.52 -5.72 1.10e+00 8.26e-01 2.71e+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 - 0.094: 2151 0.094 - 0.188: 79 0.188 - 0.281: 6 0.281 - 0.375: 0 0.375 - 0.469: 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 5.50e+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 0.27 2.00e-01 2.50e+01 1.78e+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: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.400 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.340 ------------------------------------------------------------------------------- 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= 0.236 Angle : 0.626 11.573 19242 Z= 0.490 Chirality : 0.041 0.469 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 0.00315 / 0.24 (13733) covalent geometry : angle 0.62565 / 0.49 (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 : 0.293 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: 0.5854 (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: 0.5877 (m) REVERT: A 1246 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7312 (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: 0.7073 (tppt) outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 0.4763 time to fit residues: 47.9789 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 : 0.340 ------------------------------------------------------------------------------- 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: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.0030 overall best weight: 1.7196 ------------------------------------------------------------------------------- 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 = 0.4681 r_free = 0.4681 target = 0.235866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.191142 restraints weight = 13484.170| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 1.71 r_work: 0.4045 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 13733 Z= 0.239 Angle : 0.643 8.076 19242 Z= 0.370 Chirality : 0.046 0.478 2237 Planarity : 0.006 0.120 1913 Dihedral : 23.210 179.108 3518 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.96 % Favored : 93.71 % Rotamer: Outliers : 3.44 % Allowed : 14.04 % Favored : 82.52 % 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: 0.13 (0.24), residues: 1225 helix: 1.05 (0.22), residues: 570 sheet: 0.36 (0.49), residues: 108 loop : -0.98 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1159 TYR 0.013 0.002 TYR A 281 PHE 0.019 0.002 PHE A 242 TRP 0.018 0.002 TRP A 516 HIS 0.008 0.002 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 (13733) covalent geometry : angle 0.64271 / 0.37 (19242) hydrogen bonds : bond 0.05955 / 3.97 ( 582) hydrogen bonds : angle 4.63380 / 3.33 ( 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 123 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 85 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 288 LYS cc_start: 0.7620 (tmtm) cc_final: 0.7187 (mmtt) REVERT: A 292 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7026 (tp40) REVERT: A 308 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7632 (mt) REVERT: A 381 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7474 (mtt-85) REVERT: A 461 GLN cc_start: 0.6806 (mm-40) cc_final: 0.6326 (tp-100) REVERT: A 467 ASP cc_start: 0.7289 (t0) cc_final: 0.6984 (t70) REVERT: A 482 MET cc_start: 0.8411 (mtp) cc_final: 0.8110 (mtm) REVERT: A 483 GLU cc_start: 0.7888 (tt0) cc_final: 0.7296 (pt0) REVERT: A 655 ARG cc_start: 0.7218 (ttt-90) cc_final: 0.5804 (ttp-110) REVERT: A 984 MET cc_start: 0.4537 (mpp) cc_final: 0.4236 (mpp) REVERT: A 987 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5889 (tp30) REVERT: A 994 LYS cc_start: 0.8017 (pttm) cc_final: 0.7578 (ptmm) REVERT: A 1010 MET cc_start: 0.7891 (mpt) cc_final: 0.7656 (mpt) REVERT: A 1044 LYS cc_start: 0.7752 (ptpt) cc_final: 0.7367 (pttt) REVERT: A 1121 ASN cc_start: 0.7771 (t0) cc_final: 0.7301 (t0) REVERT: A 1122 ARG cc_start: 0.7350 (mmm160) cc_final: 0.6517 (mtp180) REVERT: A 1186 THR cc_start: 0.6388 (OUTLIER) cc_final: 0.6119 (m) REVERT: A 1246 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7382 (t0) REVERT: A 1257 LYS cc_start: 0.8038 (mmmt) cc_final: 0.7312 (mtmt) REVERT: A 1285 LYS cc_start: 0.7914 (ptpt) cc_final: 0.7549 (mmmt) REVERT: A 1347 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7265 (tppt) outliers start: 38 outliers final: 12 residues processed: 116 average time/residue: 0.4941 time to fit residues: 63.0774 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 : 0.239 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 36 optimal weight: 0.0370 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.7864 ------------------------------------------------------------------------------- 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 = 0.4660 r_free = 0.4660 target = 0.233667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.188809 restraints weight = 13578.136| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 1.71 r_work: 0.4028 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3913 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 13733 Z= 0.240 Angle : 0.634 8.127 19242 Z= 0.367 Chirality : 0.046 0.491 2237 Planarity : 0.006 0.120 1913 Dihedral : 23.347 179.586 3516 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.55 % Favored : 94.04 % Rotamer: Outliers : 4.17 % Allowed : 14.58 % Favored : 81.25 % 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: -0.02 (0.24), residues: 1225 helix: 0.95 (0.22), residues: 568 sheet: 0.42 (0.49), residues: 111 loop : -1.12 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1159 TYR 0.023 0.002 TYR A1194 PHE 0.019 0.002 PHE A 66 TRP 0.017 0.002 TRP A 355 HIS 0.008 0.002 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 (13733) covalent geometry : angle 0.63360 / 0.37 (19242) hydrogen bonds : bond 0.06050 / 4.03 ( 582) hydrogen bonds : angle 4.66406 / 3.34 ( 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 132 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 86 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.8167 (mmm) cc_final: 0.7959 (mmp) REVERT: A 288 LYS cc_start: 0.7691 (tmtm) cc_final: 0.7087 (mmtt) REVERT: A 292 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7030 (tp40) REVERT: A 368 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7606 (tt) REVERT: A 381 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7240 (mtt-85) REVERT: A 461 GLN cc_start: 0.6794 (mm-40) cc_final: 0.6240 (tp-100) REVERT: A 467 ASP cc_start: 0.7350 (t0) cc_final: 0.7096 (t70) REVERT: A 482 MET cc_start: 0.8383 (mtp) cc_final: 0.8118 (mtm) REVERT: A 655 ARG cc_start: 0.7195 (ttt-90) cc_final: 0.5743 (ttp-110) REVERT: A 987 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5703 (tp30) REVERT: A 994 LYS cc_start: 0.8115 (pttm) cc_final: 0.7631 (ptmm) REVERT: A 1044 LYS cc_start: 0.7831 (ptpt) cc_final: 0.7383 (pttt) REVERT: A 1121 ASN cc_start: 0.7751 (t0) cc_final: 0.7230 (t0) REVERT: A 1122 ARG cc_start: 0.7301 (mmm160) cc_final: 0.6540 (mmm-85) REVERT: A 1186 THR cc_start: 0.6424 (OUTLIER) cc_final: 0.6142 (m) REVERT: A 1246 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7323 (t0) REVERT: A 1257 LYS cc_start: 0.8048 (mmmt) cc_final: 0.7288 (mtmt) REVERT: A 1285 LYS cc_start: 0.7981 (ptpt) cc_final: 0.7495 (tptm) REVERT: A 1347 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7088 (tppt) outliers start: 46 outliers final: 18 residues processed: 123 average time/residue: 0.4290 time to fit residues: 58.5313 Evaluate side-chains 101 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 356 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 890 ARG Chi-restraints excluded: chain A residue 900 ASN 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 1238 ILE 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 1290 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1347 LYS Chi-restraints excluded: chain A residue 1380 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 113 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 ASN A 408 GLN A 607 ASN A1323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.234102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.189238 restraints weight = 13484.987| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 1.65 r_work: 0.4036 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3921 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 13733 Z= 0.216 Angle : 0.607 8.100 19242 Z= 0.353 Chirality : 0.045 0.481 2237 Planarity : 0.005 0.120 1913 Dihedral : 23.358 178.591 3514 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.12 % Favored : 93.55 % Rotamer: Outliers : 4.80 % Allowed : 15.49 % 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: -0.00 (0.24), residues: 1225 helix: 1.03 (0.22), residues: 562 sheet: 0.35 (0.48), residues: 111 loop : -1.16 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1211 TYR 0.015 0.002 TYR A 281 PHE 0.019 0.002 PHE A 242 TRP 0.016 0.002 TRP A 355 HIS 0.006 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 (13733) covalent geometry : angle 0.60686 / 0.35 (19242) hydrogen bonds : bond 0.05816 / 3.89 ( 582) hydrogen bonds : angle 4.58756 / 3.29 ( 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 137 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 84 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.8188 (mmm) cc_final: 0.7957 (mmp) REVERT: A 288 LYS cc_start: 0.7687 (tmtm) cc_final: 0.7126 (mmtt) REVERT: A 292 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7032 (tp40) REVERT: A 451 HIS cc_start: 0.3643 (OUTLIER) cc_final: 0.0531 (m-70) REVERT: A 461 GLN cc_start: 0.6797 (mm-40) cc_final: 0.6277 (tp-100) REVERT: A 467 ASP cc_start: 0.7347 (t0) cc_final: 0.7078 (t70) REVERT: A 482 MET cc_start: 0.8369 (mtp) cc_final: 0.8093 (mtm) REVERT: A 655 ARG cc_start: 0.7157 (ttt-90) cc_final: 0.5689 (ttp-110) REVERT: A 660 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7075 (mmm-85) REVERT: A 984 MET cc_start: 0.4635 (mpp) cc_final: 0.4294 (mpp) REVERT: A 987 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5713 (tp30) REVERT: A 994 LYS cc_start: 0.8143 (pttm) cc_final: 0.7485 (ptmm) REVERT: A 1044 LYS cc_start: 0.7843 (ptpt) cc_final: 0.7364 (pttt) REVERT: A 1121 ASN cc_start: 0.7768 (t0) cc_final: 0.7210 (t0) REVERT: A 1122 ARG cc_start: 0.7312 (mmm160) cc_final: 0.6547 (mmm-85) REVERT: A 1186 THR cc_start: 0.6422 (OUTLIER) cc_final: 0.5962 (m) REVERT: A 1246 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7280 (t0) REVERT: A 1257 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7273 (mtmt) REVERT: A 1285 LYS cc_start: 0.7973 (ptpt) cc_final: 0.7504 (tptm) REVERT: A 1288 GLN cc_start: 0.6636 (OUTLIER) cc_final: 0.5553 (tm-30) REVERT: A 1308 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7474 (mtpp) REVERT: A 1347 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7159 (tppt) outliers start: 53 outliers final: 25 residues processed: 128 average time/residue: 0.4961 time to fit residues: 69.9448 Evaluate side-chains 112 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 79 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 211 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 446 ASP 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 650 PHE Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 890 ARG 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 1202 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 119 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 57 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4664 r_free = 0.4664 target = 0.233735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.188846 restraints weight = 13451.053| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 1.64 r_work: 0.4036 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 13733 Z= 0.211 Angle : 0.604 8.060 19242 Z= 0.351 Chirality : 0.045 0.477 2237 Planarity : 0.005 0.120 1913 Dihedral : 23.380 178.685 3514 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.71 % Favored : 93.96 % Rotamer: Outliers : 4.62 % Allowed : 16.76 % Favored : 78.62 % 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: 0.01 (0.24), residues: 1225 helix: 1.05 (0.22), residues: 562 sheet: 0.55 (0.49), residues: 107 loop : -1.22 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1211 TYR 0.018 0.002 TYR A 257 PHE 0.019 0.002 PHE A 242 TRP 0.017 0.002 TRP A 355 HIS 0.006 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (13733) covalent geometry : angle 0.60405 / 0.35 (19242) hydrogen bonds : bond 0.05768 / 3.86 ( 582) hydrogen bonds : angle 4.55093 / 3.27 ( 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 135 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 84 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.8235 (mmm) cc_final: 0.7980 (mmp) REVERT: A 288 LYS cc_start: 0.7649 (tmtm) cc_final: 0.7201 (mmtt) REVERT: A 292 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7025 (tp40) REVERT: A 451 HIS cc_start: 0.3676 (OUTLIER) cc_final: 0.0520 (m-70) REVERT: A 461 GLN cc_start: 0.6766 (mm-40) cc_final: 0.6260 (tp-100) REVERT: A 467 ASP cc_start: 0.7318 (t0) cc_final: 0.7066 (t70) REVERT: A 482 MET cc_start: 0.8328 (mtp) cc_final: 0.8081 (mtm) REVERT: A 655 ARG cc_start: 0.7044 (ttt-90) cc_final: 0.5656 (ttp-110) REVERT: A 660 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7006 (mmm-85) REVERT: A 961 ILE cc_start: 0.2190 (OUTLIER) cc_final: 0.1835 (mt) REVERT: A 987 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.5728 (tp30) REVERT: A 994 LYS cc_start: 0.8157 (pttm) cc_final: 0.7491 (ptmm) REVERT: A 1044 LYS cc_start: 0.7896 (ptpt) cc_final: 0.7407 (pttt) REVERT: A 1121 ASN cc_start: 0.7794 (t0) cc_final: 0.7223 (t0) REVERT: A 1122 ARG cc_start: 0.7332 (mmm160) cc_final: 0.6571 (mmm-85) REVERT: A 1186 THR cc_start: 0.6431 (OUTLIER) cc_final: 0.6052 (m) REVERT: A 1246 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7254 (t70) REVERT: A 1257 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7315 (mtmt) REVERT: A 1285 LYS cc_start: 0.7994 (ptpt) cc_final: 0.7558 (tptm) REVERT: A 1288 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.5510 (tm-30) REVERT: A 1308 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7455 (mtpp) REVERT: A 1347 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7179 (tppt) outliers start: 51 outliers final: 24 residues processed: 126 average time/residue: 0.4592 time to fit residues: 64.0581 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 : 0.317 ------------------------------------------------------------------------------- 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 374 THR 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 660 ARG Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1132 LYS 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 1205 LEU Chi-restraints excluded: chain A residue 1238 ILE 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 Chi-restraints excluded: chain A residue 1367 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4681 r_free = 0.4681 target = 0.235925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.192088 restraints weight = 13426.943| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 1.66 r_work: 0.4063 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1550 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= 0.160 Angle : 0.561 7.777 19242 Z= 0.331 Chirality : 0.042 0.451 2237 Planarity : 0.005 0.120 1913 Dihedral : 23.370 179.461 3514 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.80 % Favored : 93.88 % Rotamer: Outliers : 4.89 % Allowed : 17.12 % Favored : 77.99 % 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: 1.15 (0.22), residues: 565 sheet: 0.70 (0.50), residues: 101 loop : -1.14 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 381 TYR 0.016 0.002 TYR A1194 PHE 0.018 0.001 PHE A 242 TRP 0.020 0.002 TRP A 355 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (13733) covalent geometry : angle 0.56075 / 0.33 (19242) hydrogen bonds : bond 0.05437 / 3.64 ( 582) hydrogen bonds : angle 4.41089 / 3.17 ( 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 141 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 87 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.8166 (mmm) cc_final: 0.7901 (mmp) REVERT: A 288 LYS cc_start: 0.7576 (tmtm) cc_final: 0.7098 (mtmm) REVERT: A 292 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7006 (tp40) REVERT: A 317 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: A 451 HIS cc_start: 0.3517 (OUTLIER) cc_final: 0.0381 (m-70) REVERT: A 457 ASP cc_start: 0.5718 (OUTLIER) cc_final: 0.5425 (t0) REVERT: A 461 GLN cc_start: 0.6733 (mm-40) cc_final: 0.6151 (tp-100) REVERT: A 467 ASP cc_start: 0.7321 (t0) cc_final: 0.7053 (t70) REVERT: A 482 MET cc_start: 0.8274 (mtp) cc_final: 0.8025 (mtm) REVERT: A 655 ARG cc_start: 0.7045 (ttt-90) cc_final: 0.5641 (ttp-110) REVERT: A 660 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7034 (mmm-85) REVERT: A 987 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5608 (tp30) REVERT: A 994 LYS cc_start: 0.8117 (pttm) cc_final: 0.7449 (ptmm) REVERT: A 1044 LYS cc_start: 0.7873 (ptpt) cc_final: 0.7381 (pttt) REVERT: A 1121 ASN cc_start: 0.7809 (t0) cc_final: 0.7181 (t0) REVERT: A 1122 ARG cc_start: 0.7322 (mmm160) cc_final: 0.6454 (mtp180) REVERT: A 1186 THR cc_start: 0.6414 (OUTLIER) cc_final: 0.6068 (m) REVERT: A 1246 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7259 (t0) REVERT: A 1257 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7313 (mtmt) REVERT: A 1285 LYS cc_start: 0.8001 (ptpt) cc_final: 0.7563 (tptm) REVERT: A 1288 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.5596 (tm-30) REVERT: A 1347 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7139 (tppt) outliers start: 54 outliers final: 19 residues processed: 132 average time/residue: 0.4598 time to fit residues: 67.3845 Evaluate side-chains 111 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 660 ARG 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 1186 THR 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 1347 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 114 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.4663 r_free = 0.4663 target = 0.233612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.189215 restraints weight = 13319.011| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 1.68 r_work: 0.4031 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1688 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= 0.213 Angle : 0.608 7.965 19242 Z= 0.352 Chirality : 0.045 0.467 2237 Planarity : 0.005 0.120 1913 Dihedral : 23.392 179.121 3514 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.20 % Favored : 93.47 % Rotamer: Outliers : 4.62 % Allowed : 17.66 % Favored : 77.72 % 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: -0.01 (0.24), residues: 1225 helix: 1.06 (0.22), residues: 561 sheet: 0.50 (0.48), residues: 107 loop : -1.24 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 890 TYR 0.017 0.002 TYR A1194 PHE 0.020 0.002 PHE A 242 TRP 0.022 0.002 TRP A 355 HIS 0.006 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (13733) covalent geometry : angle 0.60840 / 0.35 (19242) hydrogen bonds : bond 0.05723 / 3.83 ( 582) hydrogen bonds : angle 4.49863 / 3.22 ( 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 135 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 84 time to evaluate : 0.458 Fit side-chains REVERT: A 11 MET cc_start: 0.7337 (mmm) cc_final: 0.6530 (mtp) REVERT: A 50 MET cc_start: 0.8207 (mmm) cc_final: 0.7942 (mmp) REVERT: A 288 LYS cc_start: 0.7574 (tmtm) cc_final: 0.7125 (mtmm) REVERT: A 292 GLN cc_start: 0.7833 (tm-30) cc_final: 0.7028 (tp40) REVERT: A 317 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: A 451 HIS cc_start: 0.3684 (OUTLIER) cc_final: 0.0591 (m-70) REVERT: A 457 ASP cc_start: 0.5788 (OUTLIER) cc_final: 0.5503 (t0) REVERT: A 461 GLN cc_start: 0.6707 (mm-40) cc_final: 0.6225 (tp-100) REVERT: A 467 ASP cc_start: 0.7317 (t0) cc_final: 0.7082 (t70) REVERT: A 482 MET cc_start: 0.8341 (mtp) cc_final: 0.8089 (mtm) REVERT: A 655 ARG cc_start: 0.7022 (ttt-90) cc_final: 0.5651 (ttp-110) REVERT: A 660 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7031 (mmm-85) REVERT: A 961 ILE cc_start: 0.2266 (OUTLIER) cc_final: 0.1911 (mt) REVERT: A 984 MET cc_start: 0.4962 (mpp) cc_final: 0.4644 (mpp) REVERT: A 987 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5588 (tp30) REVERT: A 994 LYS cc_start: 0.8158 (pttm) cc_final: 0.7504 (ptmm) REVERT: A 1044 LYS cc_start: 0.7839 (ptpt) cc_final: 0.7339 (pttt) REVERT: A 1122 ARG cc_start: 0.7345 (mmm160) cc_final: 0.6442 (mtp180) REVERT: A 1186 THR cc_start: 0.6478 (OUTLIER) cc_final: 0.6191 (m) REVERT: A 1246 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7269 (t70) REVERT: A 1257 LYS cc_start: 0.8059 (mmmt) cc_final: 0.7301 (mtmt) REVERT: A 1285 LYS cc_start: 0.8019 (ptpt) cc_final: 0.7561 (tptm) REVERT: A 1288 GLN cc_start: 0.6692 (OUTLIER) cc_final: 0.5530 (tm-30) REVERT: A 1308 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7472 (mtpp) REVERT: A 1347 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7169 (tppt) outliers start: 51 outliers final: 20 residues processed: 127 average time/residue: 0.5337 time to fit residues: 74.8094 Evaluate side-chains 113 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 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 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 657 ILE Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 961 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 29 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1121 ASN A1144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.233422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.188859 restraints weight = 13266.212| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 1.59 r_work: 0.4040 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1772 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= 0.210 Angle : 0.603 7.948 19242 Z= 0.350 Chirality : 0.045 0.466 2237 Planarity : 0.005 0.120 1913 Dihedral : 23.416 179.059 3514 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.80 % Favored : 93.88 % Rotamer: Outliers : 4.08 % Allowed : 18.21 % Favored : 77.72 % 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: -0.05 (0.24), residues: 1225 helix: 1.02 (0.22), residues: 563 sheet: 0.44 (0.48), residues: 105 loop : -1.25 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 890 TYR 0.017 0.002 TYR A1194 PHE 0.020 0.002 PHE A1356 TRP 0.018 0.002 TRP A 355 HIS 0.006 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (13733) covalent geometry : angle 0.60339 / 0.35 (19242) hydrogen bonds : bond 0.05704 / 3.82 ( 582) hydrogen bonds : angle 4.50073 / 3.22 ( 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 124 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 79 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8228 (mmm) cc_final: 0.7961 (mmp) REVERT: A 288 LYS cc_start: 0.7559 (tmtm) cc_final: 0.7147 (mtmm) REVERT: A 292 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7041 (tp40) REVERT: A 317 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: A 451 HIS cc_start: 0.3711 (OUTLIER) cc_final: 0.0602 (m-70) REVERT: A 457 ASP cc_start: 0.5780 (OUTLIER) cc_final: 0.5477 (t0) REVERT: A 461 GLN cc_start: 0.6729 (mm-40) cc_final: 0.6143 (tp-100) REVERT: A 467 ASP cc_start: 0.7274 (t0) cc_final: 0.7057 (t70) REVERT: A 482 MET cc_start: 0.8347 (mtp) cc_final: 0.8070 (mtm) REVERT: A 655 ARG cc_start: 0.7057 (ttt-90) cc_final: 0.5693 (ttp-110) REVERT: A 660 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7130 (mmm-85) REVERT: A 668 LEU cc_start: 0.7832 (mt) cc_final: 0.7289 (pp) REVERT: A 984 MET cc_start: 0.4882 (mpp) cc_final: 0.4548 (mpp) REVERT: A 987 GLU cc_start: 0.6141 (OUTLIER) cc_final: 0.5487 (mm-30) REVERT: A 994 LYS cc_start: 0.8178 (pttm) cc_final: 0.7542 (ptmm) REVERT: A 1044 LYS cc_start: 0.7868 (ptpt) cc_final: 0.7376 (pttt) REVERT: A 1121 ASN cc_start: 0.7641 (t0) cc_final: 0.7190 (t0) REVERT: A 1186 THR cc_start: 0.6447 (OUTLIER) cc_final: 0.6192 (m) REVERT: A 1246 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7254 (t70) REVERT: A 1257 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7339 (mtmt) REVERT: A 1285 LYS cc_start: 0.8024 (ptpt) cc_final: 0.7562 (tptm) REVERT: A 1288 GLN cc_start: 0.6681 (OUTLIER) cc_final: 0.5425 (tm-30) REVERT: A 1308 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7495 (mtpp) REVERT: A 1347 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7159 (tppt) outliers start: 45 outliers final: 21 residues processed: 116 average time/residue: 0.5102 time to fit residues: 65.1301 Evaluate side-chains 108 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 459 VAL Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 883 LYS 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 133 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 33 optimal weight: 0.0020 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: 0.9990 chunk 28 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.4693 r_free = 0.4693 target = 0.237269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.193924 restraints weight = 13532.728| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 1.57 r_work: 0.4080 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3965 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1701 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= 0.147 Angle : 0.555 7.604 19242 Z= 0.327 Chirality : 0.042 0.435 2237 Planarity : 0.005 0.119 1913 Dihedral : 23.395 179.857 3514 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.47 % Favored : 94.20 % Rotamer: Outliers : 3.26 % Allowed : 19.11 % Favored : 77.63 % 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: 1.19 (0.22), residues: 565 sheet: 0.64 (0.50), residues: 101 loop : -1.12 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1211 TYR 0.017 0.002 TYR A1194 PHE 0.022 0.001 PHE A1356 TRP 0.017 0.002 TRP A 355 HIS 0.004 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (13733) covalent geometry : angle 0.55542 / 0.33 (19242) hydrogen bonds : bond 0.05303 / 3.55 ( 582) hydrogen bonds : angle 4.34380 / 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 123 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8174 (mmm) cc_final: 0.7892 (mmp) REVERT: A 288 LYS cc_start: 0.7498 (tmtm) cc_final: 0.7075 (mtmm) REVERT: A 292 GLN cc_start: 0.7799 (tm-30) cc_final: 0.6993 (tp40) REVERT: A 317 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: A 457 ASP cc_start: 0.5569 (OUTLIER) cc_final: 0.5296 (t0) REVERT: A 461 GLN cc_start: 0.6691 (mm-40) cc_final: 0.6120 (tp-100) REVERT: A 467 ASP cc_start: 0.7288 (t0) cc_final: 0.7035 (t70) REVERT: A 482 MET cc_start: 0.8288 (mtp) cc_final: 0.8028 (mtm) REVERT: A 491 MET cc_start: 0.7225 (ptm) cc_final: 0.6947 (ptm) REVERT: A 655 ARG cc_start: 0.7007 (ttt-90) cc_final: 0.5600 (ttp-110) REVERT: A 660 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7093 (mmm-85) REVERT: A 668 LEU cc_start: 0.7790 (mt) cc_final: 0.7257 (pp) REVERT: A 890 ARG cc_start: 0.7143 (mpt-90) cc_final: 0.6763 (mpt-90) REVERT: A 984 MET cc_start: 0.4550 (mpp) cc_final: 0.4227 (mpp) REVERT: A 987 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5562 (tp30) REVERT: A 994 LYS cc_start: 0.8097 (pttm) cc_final: 0.7417 (ptmm) REVERT: A 1044 LYS cc_start: 0.7831 (ptpt) cc_final: 0.7325 (pttt) REVERT: A 1121 ASN cc_start: 0.7669 (t0) cc_final: 0.7155 (t0) REVERT: A 1246 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7201 (t70) REVERT: A 1257 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7293 (mtmt) REVERT: A 1285 LYS cc_start: 0.8029 (ptpt) cc_final: 0.7547 (tptm) REVERT: A 1288 GLN cc_start: 0.6653 (OUTLIER) cc_final: 0.5540 (tm-30) REVERT: A 1347 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7115 (tppt) outliers start: 36 outliers final: 19 residues processed: 115 average time/residue: 0.5460 time to fit residues: 69.1710 Evaluate side-chains 109 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 503 ASN Chi-restraints excluded: chain A residue 660 ARG 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 1186 THR 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 1347 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 65 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4684 r_free = 0.4684 target = 0.236215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.192585 restraints weight = 13481.043| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 1.61 r_work: 0.4069 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1759 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= 0.164 Angle : 0.572 7.611 19242 Z= 0.334 Chirality : 0.042 0.436 2237 Planarity : 0.005 0.119 1913 Dihedral : 23.366 179.823 3514 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.80 % Favored : 93.96 % Rotamer: Outliers : 2.90 % Allowed : 19.75 % Favored : 77.36 % 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: 1.23 (0.22), residues: 563 sheet: 0.32 (0.48), residues: 110 loop : -1.13 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1211 TYR 0.023 0.002 TYR A1194 PHE 0.019 0.001 PHE A1356 TRP 0.018 0.002 TRP A 355 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (13733) covalent geometry : angle 0.57216 / 0.33 (19242) hydrogen bonds : bond 0.05352 / 3.58 ( 582) hydrogen bonds : angle 4.33955 / 3.12 ( 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 113 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 11 MET cc_start: 0.7346 (mmm) cc_final: 0.6544 (mtp) REVERT: A 50 MET cc_start: 0.8228 (mmm) cc_final: 0.7953 (mmp) REVERT: A 288 LYS cc_start: 0.7526 (tmtm) cc_final: 0.7126 (mtmm) REVERT: A 292 GLN cc_start: 0.7769 (tm-30) cc_final: 0.6976 (tp40) REVERT: A 317 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: A 457 ASP cc_start: 0.5531 (OUTLIER) cc_final: 0.5258 (t0) REVERT: A 461 GLN cc_start: 0.6661 (mm-40) cc_final: 0.6085 (tp-100) REVERT: A 467 ASP cc_start: 0.7293 (t0) cc_final: 0.7034 (t70) REVERT: A 482 MET cc_start: 0.8328 (mtp) cc_final: 0.8027 (mtm) REVERT: A 645 ASP cc_start: 0.7526 (t0) cc_final: 0.7315 (t0) REVERT: A 655 ARG cc_start: 0.7034 (ttt-90) cc_final: 0.5625 (ttp-110) REVERT: A 660 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7039 (mmm-85) REVERT: A 668 LEU cc_start: 0.7776 (mt) cc_final: 0.7255 (pp) REVERT: A 984 MET cc_start: 0.4383 (mpp) cc_final: 0.4074 (mpp) REVERT: A 987 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5552 (tp30) REVERT: A 994 LYS cc_start: 0.8117 (pttm) cc_final: 0.7434 (ptmm) REVERT: A 1044 LYS cc_start: 0.7807 (ptpt) cc_final: 0.7356 (pttt) REVERT: A 1121 ASN cc_start: 0.7668 (t0) cc_final: 0.7134 (t0) REVERT: A 1246 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7228 (t70) REVERT: A 1257 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7273 (mtmt) REVERT: A 1285 LYS cc_start: 0.8029 (ptpt) cc_final: 0.7543 (tptm) REVERT: A 1288 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.5501 (tm-30) REVERT: A 1347 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7129 (tppt) outliers start: 32 outliers final: 23 residues processed: 107 average time/residue: 0.5359 time to fit residues: 63.0320 Evaluate side-chains 110 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 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 1245 ASN Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1253 VAL 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 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: 0.7980 chunk 16 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.235455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.191533 restraints weight = 13415.302| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 1.61 r_work: 0.4061 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3945 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1817 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= 0.180 Angle : 0.585 7.651 19242 Z= 0.339 Chirality : 0.043 0.440 2237 Planarity : 0.005 0.119 1913 Dihedral : 23.349 179.884 3514 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.80 % Favored : 93.96 % Rotamer: Outliers : 3.26 % Allowed : 19.57 % Favored : 77.17 % 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: 0.12 (0.24), residues: 1225 helix: 1.19 (0.22), residues: 563 sheet: 0.33 (0.48), residues: 108 loop : -1.15 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1198 TYR 0.019 0.002 TYR A1194 PHE 0.020 0.002 PHE A 242 TRP 0.025 0.002 TRP A 355 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (13733) covalent geometry : angle 0.58548 / 0.34 (19242) hydrogen bonds : bond 0.05418 / 3.63 ( 582) hydrogen bonds : angle 4.37282 / 3.14 ( 1556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4053.93 seconds wall clock time: 69 minutes 55.89 seconds (4195.89 seconds total)