Starting phenix.real_space_refine on Fri Sep 11 12:17:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6s7p_10111/09_2026/6s7p_10111.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s7p_10111/09_2026/6s7p_10111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6s7p_10111/09_2026/6s7p_10111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s7p_10111/09_2026/6s7p_10111.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6s7p_10111/09_2026/6s7p_10111.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6s7p_10111/09_2026/6s7p_10111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s7p_10111/09_2026/6s7p_10111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s7p_10111/09_2026/6s7p_10111.map" } resolution = 3.2 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= 0.004 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 6 5.49 5 Mg 1 5.21 5 S 30 5.16 5 C 5864 2.51 5 N 1493 2.21 5 O 1634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9028 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1128, 8741 Classifications: {'peptide': 1128} Link IDs: {'PTRANS': 28, 'TRANS': 1099} Chain breaks: 2 Chain: "A" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 287 Unusual residues: {' MG': 1, 'ATP': 2, 'CLR': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Time building chain proxies: 2.17, per 1000 atoms: 0.24 Number of scatterers: 9028 At special positions: 0 Unit cell: (100.8, 115.92, 116.76, 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 30 16.00 P 6 15.00 Mg 1 11.99 O 1634 8.00 N 1493 7.00 C 5864 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: 0.97 Conformation dependent library (CDL) restraints added in 352.0 milliseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 6 sheets defined 69.9% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 50 through 69 removed outlier: 3.576A pdb=" N SER A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.540A pdb=" N LEU A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 107 through 160 removed outlier: 3.874A pdb=" N VAL A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TRP A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 168 removed outlier: 3.720A pdb=" N ILE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 188 Processing helix chain 'A' and resid 189 through 213 removed outlier: 4.231A pdb=" N GLY A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 222 removed outlier: 3.745A pdb=" N THR A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 218 " --> pdb=" O TRP A 214 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 262 removed outlier: 3.616A pdb=" N ALA A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 269 removed outlier: 3.730A pdb=" N VAL A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 325 removed outlier: 4.007A pdb=" N HIS A 282 " --> pdb=" O ARG A 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 321 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 322 " --> pdb=" O TYR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 350 removed outlier: 3.615A pdb=" N ALA A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 373 removed outlier: 4.126A pdb=" N TYR A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N VAL A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 443 removed outlier: 3.929A pdb=" N GLN A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 485 through 495 removed outlier: 4.025A pdb=" N ARG A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.728A pdb=" N ILE A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.075A pdb=" N THR A 524 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 534 through 548 removed outlier: 3.502A pdb=" N LYS A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 540 " --> pdb=" O GLY A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 579 removed outlier: 3.670A pdb=" N ARG A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 619 Processing helix chain 'A' and resid 622 through 629 removed outlier: 3.734A pdb=" N LYS A 626 " --> pdb=" O GLY A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 removed outlier: 3.668A pdb=" N VAL A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 723 Processing helix chain 'A' and resid 723 through 739 removed outlier: 3.656A pdb=" N ALA A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 730 " --> pdb=" O PRO A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 796 removed outlier: 3.693A pdb=" N ILE A 753 " --> pdb=" O GLN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 805 removed outlier: 3.690A pdb=" N PHE A 803 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 829 removed outlier: 3.582A pdb=" N LEU A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 818 " --> pdb=" O SER A 814 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 853 removed outlier: 3.595A pdb=" N ILE A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 861 removed outlier: 3.759A pdb=" N THR A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 858 " --> pdb=" O TRP A 854 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A 859 " --> pdb=" O GLN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 902 removed outlier: 3.855A pdb=" N GLY A 880 " --> pdb=" O LYS A 876 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 890 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 891 " --> pdb=" O LYS A 887 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 895 " --> pdb=" O ALA A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 910 Processing helix chain 'A' and resid 911 through 966 removed outlier: 5.297A pdb=" N GLY A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) Proline residue: A 926 - end of helix removed outlier: 4.027A pdb=" N SER A 951 " --> pdb=" O PHE A 947 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A 952 " --> pdb=" O MET A 948 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA A 953 " --> pdb=" O TYR A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1013 removed outlier: 4.152A pdb=" N PHE A 982 " --> pdb=" O SER A 978 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY A 988 " --> pdb=" O ALA A 984 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N HIS A 989 " --> pdb=" O VAL A 985 " (cutoff:3.500A) Proline residue: A 995 - end of helix removed outlier: 4.291A pdb=" N ALA A 998 " --> pdb=" O ALA A 994 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS A 999 " --> pdb=" O PRO A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1084 removed outlier: 3.672A pdb=" N VAL A1078 " --> pdb=" O GLY A1074 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A1079 " --> pdb=" O LYS A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1111 Processing helix chain 'A' and resid 1125 through 1132 Processing helix chain 'A' and resid 1140 through 1151 Processing helix chain 'A' and resid 1153 through 1160 Processing helix chain 'A' and resid 1169 through 1173 Processing helix chain 'A' and resid 1176 through 1190 Processing helix chain 'A' and resid 1206 through 1221 removed outlier: 3.546A pdb=" N GLU A1215 " --> pdb=" O LYS A1211 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A1216 " --> pdb=" O VAL A1212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 418 through 419 removed outlier: 3.570A pdb=" N THR A 452 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 400 through 401 Processing sheet with id=AA3, first strand: chain 'A' and resid 472 through 475 removed outlier: 4.350A pdb=" N GLU A 610 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLU A 604 " --> pdb=" O ILE A 608 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1056 through 1059 removed outlier: 3.599A pdb=" N LEU A1057 " --> pdb=" O PHE A1036 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A1092 " --> pdb=" O ASN A1037 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1040 through 1041 removed outlier: 3.575A pdb=" N PHE A1041 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1112 through 1115 removed outlier: 6.409A pdb=" N GLY A1113 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP A1199 " --> pdb=" O GLY A1113 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A1115 " --> pdb=" O ASP A1199 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A1196 " --> pdb=" O ILE A1227 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE A1229 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A1198 " --> pdb=" O ILE A1229 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU A1065 " --> pdb=" O VAL A1228 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2410 1.33 - 1.45: 1648 1.45 - 1.57: 5097 1.57 - 1.69: 10 1.69 - 1.81: 51 Bond restraints: 9216 Sorted by residual: bond pdb=" C4 ATP A1302 " pdb=" C5 ATP A1302 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.95e+01 bond pdb=" C4 ATP A1301 " pdb=" C5 ATP A1301 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.93e+01 bond pdb=" C5 ATP A1302 " pdb=" C6 ATP A1302 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.97e+01 bond pdb=" C5 ATP A1301 " pdb=" C6 ATP A1301 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.80e+01 bond pdb=" C4 ATP A1301 " pdb=" N9 ATP A1301 " ideal model delta sigma weight residual 1.374 1.318 0.056 1.00e-02 1.00e+04 3.12e+01 ... (remaining 9211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 12314 3.62 - 7.24: 184 7.24 - 10.86: 14 10.86 - 14.49: 3 14.49 - 18.11: 2 Bond angle restraints: 12517 Sorted by residual: angle pdb=" PB ATP A1301 " pdb=" O3B ATP A1301 " pdb=" PG ATP A1301 " ideal model delta sigma weight residual 139.87 121.76 18.11 1.00e+00 1.00e+00 3.28e+02 angle pdb=" PB ATP A1302 " pdb=" O3B ATP A1302 " pdb=" PG ATP A1302 " ideal model delta sigma weight residual 139.87 122.92 16.95 1.00e+00 1.00e+00 2.87e+02 angle pdb=" PA ATP A1302 " pdb=" O3A ATP A1302 " pdb=" PB ATP A1302 " ideal model delta sigma weight residual 136.83 123.18 13.65 1.00e+00 1.00e+00 1.86e+02 angle pdb=" PA ATP A1301 " pdb=" O3A ATP A1301 " pdb=" PB ATP A1301 " ideal model delta sigma weight residual 136.83 124.45 12.38 1.00e+00 1.00e+00 1.53e+02 angle pdb=" C5 ATP A1302 " pdb=" C4 ATP A1302 " pdb=" N3 ATP A1302 " ideal model delta sigma weight residual 126.80 118.08 8.72 1.00e+00 1.00e+00 7.60e+01 ... (remaining 12512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 5098 15.93 - 31.86: 225 31.86 - 47.79: 45 47.79 - 63.71: 8 63.71 - 79.64: 5 Dihedral angle restraints: 5381 sinusoidal: 2148 harmonic: 3233 Sorted by residual: dihedral pdb=" CA GLN A 520 " pdb=" C GLN A 520 " pdb=" N LYS A 521 " pdb=" CA LYS A 521 " ideal model delta harmonic sigma weight residual -180.00 -153.70 -26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA PRO A1161 " pdb=" C PRO A1161 " pdb=" N HIS A1162 " pdb=" CA HIS A1162 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA VAL A 609 " pdb=" C VAL A 609 " pdb=" N GLU A 610 " pdb=" CA GLU A 610 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1255 0.093 - 0.187: 162 0.187 - 0.280: 18 0.280 - 0.373: 11 0.373 - 0.466: 6 Chirality restraints: 1452 Sorted by residual: chirality pdb=" C14 CLR A1306 " pdb=" C13 CLR A1306 " pdb=" C15 CLR A1306 " pdb=" C8 CLR A1306 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" C14 CLR A1304 " pdb=" C13 CLR A1304 " pdb=" C15 CLR A1304 " pdb=" C8 CLR A1304 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C14 CLR A1309 " pdb=" C13 CLR A1309 " pdb=" C15 CLR A1309 " pdb=" C8 CLR A1309 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 1449 not shown) Planarity restraints: 1534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 71 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO A 72 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 994 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO A 995 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 995 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 995 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1163 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C LYS A1163 " 0.037 2.00e-02 2.50e+03 pdb=" O LYS A1163 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A1164 " -0.013 2.00e-02 2.50e+03 ... (remaining 1531 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 70 2.65 - 3.21: 7978 3.21 - 3.77: 13312 3.77 - 4.34: 18647 4.34 - 4.90: 31163 Nonbonded interactions: 71170 Sorted by model distance: nonbonded pdb=" O2G ATP A1302 " pdb="MG MG A1303 " model vdw 2.085 2.170 nonbonded pdb=" OE1 GLN A1117 " pdb="MG MG A1303 " model vdw 2.087 2.170 nonbonded pdb=" O2B ATP A1302 " pdb="MG MG A1303 " model vdw 2.088 2.170 nonbonded pdb=" NZ LYS A1075 " pdb=" O1G ATP A1302 " model vdw 2.347 3.120 nonbonded pdb=" OG SER A 483 " pdb=" OE1 GLU A 898 " model vdw 2.350 3.040 ... (remaining 71165 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.100 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.009 0.074 9216 Z= 0.439 Angle : 1.132 18.107 12517 Z= 0.664 Chirality : 0.075 0.466 1452 Planarity : 0.007 0.071 1534 Dihedral : 10.364 79.642 3307 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.33 % Allowed : 2.07 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.20), residues: 1122 helix: -1.69 (0.15), residues: 745 sheet: -1.23 (0.59), residues: 65 loop : -2.54 (0.29), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A 176 TYR 0.033 0.004 TYR A 118 PHE 0.036 0.004 PHE A 603 TRP 0.021 0.003 TRP A1107 HIS 0.010 0.002 HIS A1154 Details of bonding type rmsd/Z covalent geometry : bond 0.00926 / 0.44 ( 9216) covalent geometry : angle 1.13168 / 0.66 (12517) hydrogen bonds : bond 0.15448 / 10.58 ( 575) hydrogen bonds : angle 5.59750 / 4.18 ( 1683) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 81 MET cc_start: 0.3927 (ptt) cc_final: 0.3433 (mmp) REVERT: A 326 LYS cc_start: 0.7949 (mttt) cc_final: 0.7273 (mmmt) REVERT: A 1102 LYS cc_start: 0.7957 (mmtm) cc_final: 0.7739 (mttt) outliers start: 3 outliers final: 2 residues processed: 151 average time/residue: 0.1212 time to fit residues: 24.5066 Evaluate side-chains 88 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 775 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS A 349 GLN A 550 ASN A1053 GLN A1154 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.151016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132236 restraints weight = 10885.863| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.30 r_work: 0.3460 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9216 Z= 0.139 Angle : 0.535 9.690 12517 Z= 0.286 Chirality : 0.040 0.138 1452 Planarity : 0.004 0.036 1534 Dihedral : 6.717 74.635 1290 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.31 % Allowed : 6.20 % Favored : 92.49 % 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: -0.67 (0.24), residues: 1122 helix: 0.21 (0.18), residues: 753 sheet: -0.36 (0.69), residues: 60 loop : -1.92 (0.30), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1191 TYR 0.012 0.001 TYR A1086 PHE 0.014 0.002 PHE A1085 TRP 0.010 0.001 TRP A 317 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 9216) covalent geometry : angle 0.53519 / 0.29 (12517) hydrogen bonds : bond 0.06026 / 3.90 ( 575) hydrogen bonds : angle 4.17174 / 3.10 ( 1683) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.356 Fit side-chains REVERT: A 71 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8457 (tt) REVERT: A 81 MET cc_start: 0.4565 (ptt) cc_final: 0.3458 (mmp) REVERT: A 326 LYS cc_start: 0.8251 (mttt) cc_final: 0.7426 (mmmt) REVERT: A 591 LEU cc_start: 0.8273 (mt) cc_final: 0.7970 (tp) REVERT: A 1071 SER cc_start: 0.9016 (t) cc_final: 0.8689 (m) REVERT: A 1102 LYS cc_start: 0.8068 (mmtm) cc_final: 0.7697 (mttt) outliers start: 12 outliers final: 6 residues processed: 116 average time/residue: 0.0941 time to fit residues: 15.7679 Evaluate side-chains 93 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1092 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 88 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS A 349 GLN ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.152580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134038 restraints weight = 10786.839| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.29 r_work: 0.3481 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9216 Z= 0.119 Angle : 0.486 9.229 12517 Z= 0.257 Chirality : 0.039 0.139 1452 Planarity : 0.003 0.039 1534 Dihedral : 6.100 79.167 1289 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.85 % Allowed : 8.27 % Favored : 89.88 % 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: 0.41 (0.25), residues: 1122 helix: 1.11 (0.19), residues: 753 sheet: -0.24 (0.67), residues: 60 loop : -1.67 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 549 TYR 0.010 0.001 TYR A 852 PHE 0.016 0.001 PHE A 993 TRP 0.009 0.001 TRP A 234 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 9216) covalent geometry : angle 0.48633 / 0.26 (12517) hydrogen bonds : bond 0.05214 / 3.39 ( 575) hydrogen bonds : angle 3.86254 / 2.85 ( 1683) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.300 Fit side-chains REVERT: A 71 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8455 (tt) REVERT: A 81 MET cc_start: 0.4561 (ptt) cc_final: 0.3574 (mmp) REVERT: A 326 LYS cc_start: 0.8243 (mttt) cc_final: 0.7485 (mmmt) REVERT: A 550 ASN cc_start: 0.7614 (t0) cc_final: 0.7256 (p0) REVERT: A 949 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.6768 (t80) REVERT: A 1071 SER cc_start: 0.8963 (t) cc_final: 0.8699 (m) REVERT: A 1102 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7694 (mttt) REVERT: A 1218 ASP cc_start: 0.7859 (t0) cc_final: 0.7648 (m-30) outliers start: 17 outliers final: 7 residues processed: 113 average time/residue: 0.0836 time to fit residues: 14.0505 Evaluate side-chains 93 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 942 SER Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1195 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 0.0980 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 67 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS A 349 GLN ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.152676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134117 restraints weight = 10964.327| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.30 r_work: 0.3480 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9216 Z= 0.114 Angle : 0.464 7.763 12517 Z= 0.246 Chirality : 0.038 0.144 1452 Planarity : 0.003 0.040 1534 Dihedral : 5.824 87.751 1288 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.39 % Allowed : 8.60 % Favored : 89.01 % 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: 0.85 (0.25), residues: 1122 helix: 1.50 (0.19), residues: 753 sheet: -0.60 (0.59), residues: 70 loop : -1.55 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.020 0.001 TYR A 118 PHE 0.011 0.001 PHE A 514 TRP 0.008 0.001 TRP A 234 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 9216) covalent geometry : angle 0.46426 / 0.25 (12517) hydrogen bonds : bond 0.04934 / 3.20 ( 575) hydrogen bonds : angle 3.72357 / 2.74 ( 1683) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.333 Fit side-chains REVERT: A 326 LYS cc_start: 0.8323 (mttt) cc_final: 0.7585 (mmmt) REVERT: A 415 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8567 (tp) REVERT: A 550 ASN cc_start: 0.7553 (t0) cc_final: 0.7219 (p0) REVERT: A 591 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7857 (tp) REVERT: A 923 LEU cc_start: 0.8233 (tp) cc_final: 0.7990 (tt) REVERT: A 949 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.6878 (t80) REVERT: A 1071 SER cc_start: 0.8959 (t) cc_final: 0.8718 (m) REVERT: A 1102 LYS cc_start: 0.8057 (mmtm) cc_final: 0.7739 (mttt) outliers start: 22 outliers final: 11 residues processed: 113 average time/residue: 0.0896 time to fit residues: 14.8288 Evaluate side-chains 102 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1195 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123731 restraints weight = 11312.796| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.33 r_work: 0.3280 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 9216 Z= 0.220 Angle : 0.598 6.530 12517 Z= 0.313 Chirality : 0.044 0.176 1452 Planarity : 0.004 0.047 1534 Dihedral : 6.062 73.295 1288 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.94 % Allowed : 8.81 % Favored : 88.25 % 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: 0.40 (0.24), residues: 1122 helix: 1.13 (0.18), residues: 751 sheet: -0.87 (0.55), residues: 75 loop : -1.59 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 176 TYR 0.013 0.002 TYR A 132 PHE 0.020 0.002 PHE A 396 TRP 0.007 0.001 TRP A 164 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 ( 9216) covalent geometry : angle 0.59817 / 0.31 (12517) hydrogen bonds : bond 0.06810 / 4.40 ( 575) hydrogen bonds : angle 4.12870 / 3.03 ( 1683) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 ASP cc_start: 0.8265 (t0) cc_final: 0.7973 (t0) REVERT: A 591 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8129 (tp) REVERT: A 830 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7675 (p) REVERT: A 949 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.6827 (t80) REVERT: A 1071 SER cc_start: 0.9063 (t) cc_final: 0.8746 (m) REVERT: A 1102 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7672 (mttt) outliers start: 27 outliers final: 18 residues processed: 112 average time/residue: 0.0820 time to fit residues: 13.4399 Evaluate side-chains 103 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 801 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1195 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.147805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129042 restraints weight = 10946.441| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.31 r_work: 0.3413 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9216 Z= 0.131 Angle : 0.497 6.497 12517 Z= 0.262 Chirality : 0.040 0.146 1452 Planarity : 0.003 0.044 1534 Dihedral : 5.490 61.211 1288 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.05 % Allowed : 9.90 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.25), residues: 1122 helix: 1.50 (0.19), residues: 753 sheet: -0.63 (0.55), residues: 75 loop : -1.52 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.009 0.001 TYR A 852 PHE 0.013 0.001 PHE A 514 TRP 0.010 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9216) covalent geometry : angle 0.49679 / 0.26 (12517) hydrogen bonds : bond 0.05535 / 3.56 ( 575) hydrogen bonds : angle 3.84948 / 2.82 ( 1683) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.8375 (mttt) cc_final: 0.7669 (mmmt) REVERT: A 470 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7706 (mt-10) REVERT: A 591 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8055 (tp) REVERT: A 830 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7601 (p) REVERT: A 949 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.6916 (t80) REVERT: A 1071 SER cc_start: 0.9019 (t) cc_final: 0.8740 (m) REVERT: A 1102 LYS cc_start: 0.8032 (mmtm) cc_final: 0.7674 (mttt) outliers start: 28 outliers final: 18 residues processed: 119 average time/residue: 0.0909 time to fit residues: 15.7196 Evaluate side-chains 109 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1195 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126998 restraints weight = 11082.407| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.32 r_work: 0.3396 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9216 Z= 0.156 Angle : 0.525 6.178 12517 Z= 0.276 Chirality : 0.041 0.152 1452 Planarity : 0.003 0.047 1534 Dihedral : 5.344 61.037 1288 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.94 % Allowed : 10.77 % Favored : 86.29 % 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: 0.79 (0.25), residues: 1122 helix: 1.43 (0.19), residues: 755 sheet: -0.63 (0.55), residues: 75 loop : -1.52 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.022 0.002 TYR A 118 PHE 0.026 0.002 PHE A 316 TRP 0.010 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 9216) covalent geometry : angle 0.52537 / 0.28 (12517) hydrogen bonds : bond 0.05918 / 3.83 ( 575) hydrogen bonds : angle 3.91765 / 2.87 ( 1683) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.331 Fit side-chains REVERT: A 326 LYS cc_start: 0.8388 (mttt) cc_final: 0.7674 (mmmt) REVERT: A 456 ASP cc_start: 0.8293 (t0) cc_final: 0.8044 (t0) REVERT: A 591 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7941 (tp) REVERT: A 800 MET cc_start: 0.8525 (tpp) cc_final: 0.8249 (mmp) REVERT: A 830 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7645 (p) REVERT: A 949 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.6834 (t80) REVERT: A 1071 SER cc_start: 0.9033 (t) cc_final: 0.8735 (m) REVERT: A 1102 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7620 (mttt) outliers start: 27 outliers final: 17 residues processed: 111 average time/residue: 0.0933 time to fit residues: 14.9587 Evaluate side-chains 106 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1195 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130221 restraints weight = 10965.522| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.31 r_work: 0.3437 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9216 Z= 0.125 Angle : 0.490 7.539 12517 Z= 0.258 Chirality : 0.039 0.144 1452 Planarity : 0.003 0.045 1534 Dihedral : 5.056 57.752 1288 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.07 % Allowed : 11.86 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.25), residues: 1122 helix: 1.67 (0.19), residues: 756 sheet: -0.61 (0.55), residues: 75 loop : -1.42 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 595 TYR 0.010 0.001 TYR A 852 PHE 0.020 0.001 PHE A 993 TRP 0.011 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 9216) covalent geometry : angle 0.49019 / 0.26 (12517) hydrogen bonds : bond 0.05273 / 3.40 ( 575) hydrogen bonds : angle 3.77579 / 2.77 ( 1683) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.352 Fit side-chains REVERT: A 326 LYS cc_start: 0.8346 (mttt) cc_final: 0.7709 (mmmt) REVERT: A 456 ASP cc_start: 0.8243 (t0) cc_final: 0.7992 (t0) REVERT: A 591 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7996 (tp) REVERT: A 800 MET cc_start: 0.8484 (tpp) cc_final: 0.8222 (mmp) REVERT: A 830 THR cc_start: 0.7786 (OUTLIER) cc_final: 0.7584 (p) REVERT: A 949 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.7022 (t80) REVERT: A 1071 SER cc_start: 0.8981 (t) cc_final: 0.8719 (m) REVERT: A 1102 LYS cc_start: 0.8041 (mmtm) cc_final: 0.7689 (mttt) outliers start: 19 outliers final: 15 residues processed: 101 average time/residue: 0.0882 time to fit residues: 13.1841 Evaluate side-chains 102 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1195 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 929 ASN A1053 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128611 restraints weight = 11054.300| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.33 r_work: 0.3417 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9216 Z= 0.142 Angle : 0.508 7.262 12517 Z= 0.268 Chirality : 0.040 0.149 1452 Planarity : 0.003 0.046 1534 Dihedral : 5.077 58.306 1288 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.18 % Allowed : 11.86 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.25), residues: 1122 helix: 1.63 (0.19), residues: 756 sheet: -0.54 (0.55), residues: 75 loop : -1.38 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.037 0.001 TYR A 118 PHE 0.017 0.001 PHE A 316 TRP 0.009 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 9216) covalent geometry : angle 0.50757 / 0.27 (12517) hydrogen bonds : bond 0.05591 / 3.61 ( 575) hydrogen bonds : angle 3.83691 / 2.82 ( 1683) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.347 Fit side-chains REVERT: A 326 LYS cc_start: 0.8352 (mttt) cc_final: 0.7691 (mmmt) REVERT: A 456 ASP cc_start: 0.8292 (t0) cc_final: 0.8091 (t0) REVERT: A 591 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8035 (tp) REVERT: A 800 MET cc_start: 0.8504 (tpp) cc_final: 0.8238 (mmp) REVERT: A 830 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7623 (p) REVERT: A 949 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.6927 (t80) REVERT: A 1071 SER cc_start: 0.8998 (t) cc_final: 0.8736 (m) REVERT: A 1102 LYS cc_start: 0.7985 (mmtm) cc_final: 0.7611 (mttt) outliers start: 20 outliers final: 16 residues processed: 101 average time/residue: 0.0847 time to fit residues: 12.6943 Evaluate side-chains 106 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.149286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130567 restraints weight = 10955.284| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.31 r_work: 0.3443 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9216 Z= 0.126 Angle : 0.486 7.162 12517 Z= 0.258 Chirality : 0.039 0.146 1452 Planarity : 0.003 0.045 1534 Dihedral : 4.905 57.017 1288 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.29 % Allowed : 11.64 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1122 helix: 1.75 (0.19), residues: 755 sheet: -0.51 (0.55), residues: 75 loop : -1.34 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1013 TYR 0.010 0.001 TYR A 852 PHE 0.015 0.001 PHE A 316 TRP 0.010 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 9216) covalent geometry : angle 0.48618 / 0.26 (12517) hydrogen bonds : bond 0.05257 / 3.40 ( 575) hydrogen bonds : angle 3.75341 / 2.75 ( 1683) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.274 Fit side-chains REVERT: A 326 LYS cc_start: 0.8330 (mttt) cc_final: 0.7719 (mmmt) REVERT: A 591 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8008 (tp) REVERT: A 800 MET cc_start: 0.8481 (tpp) cc_final: 0.8216 (mmp) REVERT: A 830 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7582 (p) REVERT: A 949 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.6916 (t80) REVERT: A 1071 SER cc_start: 0.8976 (t) cc_final: 0.8729 (m) REVERT: A 1102 LYS cc_start: 0.7988 (mmtm) cc_final: 0.7626 (mttt) outliers start: 21 outliers final: 17 residues processed: 102 average time/residue: 0.0793 time to fit residues: 12.0894 Evaluate side-chains 106 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 106 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS A 298 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.151930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133404 restraints weight = 10823.588| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.30 r_work: 0.3478 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9216 Z= 0.113 Angle : 0.464 7.142 12517 Z= 0.246 Chirality : 0.038 0.142 1452 Planarity : 0.003 0.045 1534 Dihedral : 4.632 55.792 1288 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.50 % Allowed : 11.64 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.25), residues: 1122 helix: 1.89 (0.19), residues: 755 sheet: -0.32 (0.59), residues: 70 loop : -1.29 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1013 TYR 0.035 0.001 TYR A 118 PHE 0.013 0.001 PHE A 316 TRP 0.010 0.001 TRP A 317 HIS 0.003 0.000 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 9216) covalent geometry : angle 0.46425 / 0.25 (12517) hydrogen bonds : bond 0.04789 / 3.10 ( 575) hydrogen bonds : angle 3.65100 / 2.68 ( 1683) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2318.22 seconds wall clock time: 40 minutes 26.51 seconds (2426.51 seconds total)