Starting phenix.real_space_refine on Thu Feb 13 19:34:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s7p_10111/02_2025/6s7p_10111.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s7p_10111/02_2025/6s7p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6s7p_10111/02_2025/6s7p_10111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s7p_10111/02_2025/6s7p_10111.map" model { file = "/net/cci-nas-00/data/ceres_data/6s7p_10111/02_2025/6s7p_10111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s7p_10111/02_2025/6s7p_10111.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.71, per 1000 atoms: 0.63 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: 2.37 Conformation dependent library (CDL) restraints added in 993.9 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: 1.00 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: 3.45 Time building geometry restraints manager: 2.74 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: 5508 15.93 - 31.86: 294 31.86 - 47.79: 60 47.79 - 63.71: 22 63.71 - 79.64: 7 Dihedral angle restraints: 5891 sinusoidal: 2658 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 5888 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: 3.150 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.700 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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= 0.594 Angle : 1.132 18.107 12517 Z= 0.664 Chirality : 0.075 0.466 1452 Planarity : 0.007 0.071 1534 Dihedral : 11.278 79.642 3817 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.003 TRP A1107 HIS 0.010 0.002 HIS A1154 PHE 0.036 0.004 PHE A 603 TYR 0.033 0.004 TYR A 118 ARG 0.018 0.002 ARG A 176 *********************** 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 : 0.914 Fit side-chains revert: symmetry clash REVERT: A 81 MET cc_start: 0.3927 (ptt) cc_final: 0.3483 (mmp) REVERT: A 326 LYS cc_start: 0.7949 (mttt) cc_final: 0.7276 (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: 0.2749 time to fit residues: 54.8188 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 : 1.063 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3803 r_free = 0.3803 target = 0.151692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.132976 restraints weight = 10756.463| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.31 r_work: 0.3347 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1828 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= 0.187 Angle : 0.531 9.779 12517 Z= 0.284 Chirality : 0.040 0.137 1452 Planarity : 0.004 0.036 1534 Dihedral : 9.222 86.616 1800 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.40 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1122 helix: 0.25 (0.18), residues: 751 sheet: -0.34 (0.69), residues: 60 loop : -1.93 (0.30), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 317 HIS 0.005 0.001 HIS A 67 PHE 0.015 0.002 PHE A1085 TYR 0.012 0.001 TYR A1086 ARG 0.004 0.000 ARG A1191 *********************** 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 129 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.932 Fit side-chains REVERT: A 71 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8388 (tt) REVERT: A 81 MET cc_start: 0.4539 (ptt) cc_final: 0.3482 (mmp) REVERT: A 326 LYS cc_start: 0.8217 (mttt) cc_final: 0.7390 (mmmt) REVERT: A 328 TYR cc_start: 0.8228 (m-10) cc_final: 0.8027 (m-10) REVERT: A 415 LEU cc_start: 0.8760 (tt) cc_final: 0.8542 (tp) REVERT: A 591 LEU cc_start: 0.8240 (mt) cc_final: 0.7956 (tp) REVERT: A 1071 SER cc_start: 0.9001 (t) cc_final: 0.8676 (m) REVERT: A 1102 LYS cc_start: 0.8041 (mmtm) cc_final: 0.7654 (mttt) outliers start: 12 outliers final: 6 residues processed: 123 average time/residue: 0.2288 time to fit residues: 39.7273 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 : 0.929 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3767 r_free = 0.3767 target = 0.149054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130308 restraints weight = 11043.279| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.30 r_work: 0.3302 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9216 Z= 0.228 Angle : 0.540 8.900 12517 Z= 0.284 Chirality : 0.041 0.150 1452 Planarity : 0.003 0.042 1534 Dihedral : 8.840 86.097 1799 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.50 % Allowed : 7.73 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1122 helix: 0.88 (0.19), residues: 753 sheet: -0.81 (0.60), residues: 70 loop : -1.72 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 317 HIS 0.004 0.001 HIS A 67 PHE 0.017 0.002 PHE A 316 TYR 0.011 0.001 TYR A 852 ARG 0.003 0.000 ARG A 176 *********************** 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 117 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.947 Fit side-chains REVERT: A 81 MET cc_start: 0.4720 (ptt) cc_final: 0.3730 (mmp) REVERT: A 113 MET cc_start: 0.7703 (mmm) cc_final: 0.7495 (mtt) REVERT: A 326 LYS cc_start: 0.8226 (mttt) cc_final: 0.7446 (mmmt) REVERT: A 591 LEU cc_start: 0.8305 (mt) cc_final: 0.7737 (tp) REVERT: A 949 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.6727 (t80) REVERT: A 1071 SER cc_start: 0.9022 (t) cc_final: 0.8715 (m) REVERT: A 1102 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7651 (mttt) REVERT: A 1218 ASP cc_start: 0.7886 (t0) cc_final: 0.7671 (m-30) outliers start: 23 outliers final: 13 residues processed: 110 average time/residue: 0.2269 time to fit residues: 35.6810 Evaluate side-chains 99 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 460 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 733 SER 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 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 Chi-restraints excluded: chain A residue 1235 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.147900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.129148 restraints weight = 10866.198| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.29 r_work: 0.3425 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2407 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= 0.209 Angle : 0.509 7.791 12517 Z= 0.269 Chirality : 0.040 0.148 1452 Planarity : 0.003 0.044 1534 Dihedral : 8.544 87.920 1798 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.83 % Allowed : 8.05 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1122 helix: 1.18 (0.19), residues: 757 sheet: -0.89 (0.56), residues: 75 loop : -1.67 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 317 HIS 0.004 0.001 HIS A 67 PHE 0.014 0.002 PHE A 316 TYR 0.012 0.001 TYR A 961 ARG 0.002 0.000 ARG A 969 *********************** 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: 26 poor density : 96 time to evaluate : 0.958 Fit side-chains REVERT: A 81 MET cc_start: 0.4633 (ptt) cc_final: 0.3728 (mmp) REVERT: A 326 LYS cc_start: 0.8361 (mttt) cc_final: 0.7618 (mmmt) REVERT: A 591 LEU cc_start: 0.8286 (mt) cc_final: 0.7893 (tp) REVERT: A 949 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.6845 (t80) REVERT: A 1071 SER cc_start: 0.9033 (t) cc_final: 0.8755 (m) REVERT: A 1102 LYS cc_start: 0.8037 (mmtm) cc_final: 0.7673 (mttt) REVERT: A 1218 ASP cc_start: 0.7954 (t0) cc_final: 0.7750 (m-30) outliers start: 26 outliers final: 19 residues processed: 114 average time/residue: 0.2032 time to fit residues: 33.6457 Evaluate side-chains 102 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 594 VAL Chi-restraints excluded: chain A residue 695 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 828 THR Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1235 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 107 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.145830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.126964 restraints weight = 11169.124| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.32 r_work: 0.3298 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2546 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= 0.233 Angle : 0.525 6.437 12517 Z= 0.277 Chirality : 0.041 0.149 1452 Planarity : 0.003 0.045 1534 Dihedral : 8.471 87.665 1798 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.94 % Allowed : 9.03 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1122 helix: 1.27 (0.19), residues: 758 sheet: -0.83 (0.55), residues: 75 loop : -1.62 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 PHE 0.014 0.002 PHE A1085 TYR 0.021 0.001 TYR A 118 ARG 0.003 0.000 ARG A1013 *********************** 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 115 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.945 Fit side-chains REVERT: A 81 MET cc_start: 0.4886 (ptt) cc_final: 0.3887 (mmp) REVERT: A 326 LYS cc_start: 0.8313 (mttt) cc_final: 0.7584 (mmmt) REVERT: A 470 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7684 (mt-10) REVERT: A 591 LEU cc_start: 0.8362 (mt) cc_final: 0.7908 (tp) REVERT: A 949 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.6909 (t80) REVERT: A 1071 SER cc_start: 0.9015 (t) cc_final: 0.8734 (m) REVERT: A 1102 LYS cc_start: 0.7970 (mmtm) cc_final: 0.7607 (mttt) REVERT: A 1218 ASP cc_start: 0.7939 (t0) cc_final: 0.7711 (m-30) outliers start: 27 outliers final: 20 residues processed: 108 average time/residue: 0.1809 time to fit residues: 29.2862 Evaluate side-chains 105 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 594 VAL Chi-restraints excluded: chain A residue 695 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 775 THR Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1009 MET 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 Chi-restraints excluded: chain A residue 1235 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125926 restraints weight = 11143.482| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.31 r_work: 0.3289 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9216 Z= 0.285 Angle : 0.560 6.286 12517 Z= 0.295 Chirality : 0.042 0.153 1452 Planarity : 0.003 0.048 1534 Dihedral : 8.562 86.705 1798 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.26 % Allowed : 9.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1122 helix: 1.17 (0.19), residues: 758 sheet: -0.80 (0.55), residues: 75 loop : -1.64 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 PHE 0.015 0.002 PHE A 514 TYR 0.013 0.002 TYR A 961 ARG 0.003 0.000 ARG A1013 *********************** 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 122 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.968 Fit side-chains REVERT: A 81 MET cc_start: 0.4904 (ptt) cc_final: 0.3915 (mmp) REVERT: A 326 LYS cc_start: 0.8393 (mttt) cc_final: 0.7671 (mmmt) REVERT: A 456 ASP cc_start: 0.8284 (t0) cc_final: 0.8044 (t0) REVERT: A 591 LEU cc_start: 0.8433 (mt) cc_final: 0.7950 (tp) REVERT: A 1071 SER cc_start: 0.9048 (t) cc_final: 0.8740 (m) REVERT: A 1102 LYS cc_start: 0.8019 (mmtm) cc_final: 0.7626 (mttt) REVERT: A 1218 ASP cc_start: 0.7952 (t0) cc_final: 0.7718 (m-30) outliers start: 30 outliers final: 23 residues processed: 117 average time/residue: 0.1937 time to fit residues: 33.5715 Evaluate side-chains 108 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 594 VAL Chi-restraints excluded: chain A residue 695 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 775 THR 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 912 GLU Chi-restraints excluded: chain A residue 1009 MET 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 Chi-restraints excluded: chain A residue 1235 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.147273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128547 restraints weight = 11224.201| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.33 r_work: 0.3297 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9216 Z= 0.181 Angle : 0.497 6.866 12517 Z= 0.264 Chirality : 0.040 0.144 1452 Planarity : 0.003 0.045 1534 Dihedral : 8.332 89.824 1798 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.39 % Allowed : 10.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 1122 helix: 1.51 (0.19), residues: 758 sheet: -0.65 (0.55), residues: 75 loop : -1.56 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 317 HIS 0.004 0.001 HIS A 67 PHE 0.013 0.001 PHE A 514 TYR 0.010 0.001 TYR A 852 ARG 0.002 0.000 ARG A1013 *********************** 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 120 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 1.021 Fit side-chains REVERT: A 81 MET cc_start: 0.4923 (ptt) cc_final: 0.3975 (mmp) REVERT: A 326 LYS cc_start: 0.8351 (mttt) cc_final: 0.7637 (mmmt) REVERT: A 456 ASP cc_start: 0.8273 (t0) cc_final: 0.8017 (t0) REVERT: A 470 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7697 (mt-10) REVERT: A 499 MET cc_start: 0.7888 (tpt) cc_final: 0.7620 (tpt) REVERT: A 591 LEU cc_start: 0.8363 (mt) cc_final: 0.7885 (tp) REVERT: A 949 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.6975 (t80) REVERT: A 1071 SER cc_start: 0.9003 (t) cc_final: 0.8734 (m) REVERT: A 1102 LYS cc_start: 0.7968 (mmtm) cc_final: 0.7576 (mttt) REVERT: A 1218 ASP cc_start: 0.7899 (t0) cc_final: 0.7673 (m-30) outliers start: 22 outliers final: 19 residues processed: 113 average time/residue: 0.1923 time to fit residues: 31.5194 Evaluate side-chains 109 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 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 594 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 949 TYR Chi-restraints excluded: chain A residue 1009 MET 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 Chi-restraints excluded: chain A residue 1235 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.147233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128515 restraints weight = 11172.936| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.32 r_work: 0.3404 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9216 Z= 0.202 Angle : 0.510 6.155 12517 Z= 0.269 Chirality : 0.040 0.146 1452 Planarity : 0.003 0.047 1534 Dihedral : 8.335 89.433 1798 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.61 % Allowed : 11.21 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1122 helix: 1.51 (0.19), residues: 759 sheet: -0.59 (0.55), residues: 75 loop : -1.51 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 PHE 0.022 0.001 PHE A 316 TYR 0.032 0.001 TYR A 118 ARG 0.002 0.000 ARG A 969 *********************** 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 117 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.123 Fit side-chains REVERT: A 81 MET cc_start: 0.4975 (ptt) cc_final: 0.4070 (mmp) REVERT: A 326 LYS cc_start: 0.8370 (mttt) cc_final: 0.7691 (mmmt) REVERT: A 456 ASP cc_start: 0.8316 (t0) cc_final: 0.8045 (t0) REVERT: A 499 MET cc_start: 0.7936 (tpt) cc_final: 0.7621 (tpt) REVERT: A 949 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.6994 (t80) REVERT: A 1071 SER cc_start: 0.9012 (t) cc_final: 0.8754 (m) REVERT: A 1102 LYS cc_start: 0.8013 (mmtm) cc_final: 0.7617 (mttt) REVERT: A 1218 ASP cc_start: 0.7926 (t0) cc_final: 0.7694 (m-30) outliers start: 24 outliers final: 20 residues processed: 109 average time/residue: 0.2070 time to fit residues: 33.3274 Evaluate side-chains 110 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 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 594 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 912 GLU Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1009 MET 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 Chi-restraints excluded: chain A residue 1235 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 929 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.129047 restraints weight = 10921.293| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.30 r_work: 0.3425 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9216 Z= 0.188 Angle : 0.499 6.260 12517 Z= 0.264 Chirality : 0.040 0.145 1452 Planarity : 0.003 0.046 1534 Dihedral : 8.172 89.845 1798 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.72 % Allowed : 10.88 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1122 helix: 1.59 (0.19), residues: 759 sheet: -0.51 (0.55), residues: 75 loop : -1.42 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 PHE 0.018 0.001 PHE A 316 TYR 0.009 0.001 TYR A 852 ARG 0.002 0.000 ARG A 969 *********************** 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 116 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.947 Fit side-chains REVERT: A 81 MET cc_start: 0.4946 (ptt) cc_final: 0.4075 (mmp) REVERT: A 326 LYS cc_start: 0.8337 (mttt) cc_final: 0.7681 (mmmt) REVERT: A 456 ASP cc_start: 0.8263 (t0) cc_final: 0.8005 (t0) REVERT: A 499 MET cc_start: 0.7908 (tpt) cc_final: 0.7587 (tpt) REVERT: A 591 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8035 (tp) REVERT: A 949 TYR cc_start: 0.7703 (OUTLIER) cc_final: 0.6923 (t80) REVERT: A 1071 SER cc_start: 0.9005 (t) cc_final: 0.8762 (m) REVERT: A 1102 LYS cc_start: 0.8032 (mmtm) cc_final: 0.7627 (mttt) REVERT: A 1218 ASP cc_start: 0.7921 (t0) cc_final: 0.7686 (m-30) outliers start: 25 outliers final: 20 residues processed: 107 average time/residue: 0.1839 time to fit residues: 29.2196 Evaluate side-chains 113 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 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 912 GLU Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1009 MET 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 Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1241 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.148937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130402 restraints weight = 10988.690| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.30 r_work: 0.3437 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9216 Z= 0.175 Angle : 0.496 8.018 12517 Z= 0.260 Chirality : 0.039 0.143 1452 Planarity : 0.003 0.046 1534 Dihedral : 7.770 89.380 1798 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.50 % Allowed : 11.32 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1122 helix: 1.74 (0.19), residues: 752 sheet: -0.45 (0.56), residues: 75 loop : -1.34 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 PHE 0.018 0.001 PHE A 316 TYR 0.034 0.001 TYR A 118 ARG 0.002 0.000 ARG A 969 ********************** 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 116 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.027 Fit side-chains REVERT: A 326 LYS cc_start: 0.8350 (mttt) cc_final: 0.7709 (mmmt) REVERT: A 456 ASP cc_start: 0.8246 (t0) cc_final: 0.8046 (t0) REVERT: A 499 MET cc_start: 0.7907 (tpt) cc_final: 0.7583 (tpt) REVERT: A 591 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8069 (tp) REVERT: A 949 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.7155 (t80) REVERT: A 1071 SER cc_start: 0.8978 (t) cc_final: 0.8758 (m) REVERT: A 1102 LYS cc_start: 0.8004 (mmtm) cc_final: 0.7615 (mttt) REVERT: A 1218 ASP cc_start: 0.7917 (t0) cc_final: 0.7686 (m-30) outliers start: 23 outliers final: 20 residues processed: 108 average time/residue: 0.1990 time to fit residues: 31.7364 Evaluate side-chains 112 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 912 GLU Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1009 MET 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 Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1241 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.148573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.129904 restraints weight = 11024.267| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.31 r_work: 0.3433 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9216 Z= 0.187 Angle : 0.503 8.333 12517 Z= 0.265 Chirality : 0.040 0.145 1452 Planarity : 0.003 0.046 1534 Dihedral : 7.747 89.640 1798 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.39 % Allowed : 11.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1122 helix: 1.72 (0.19), residues: 754 sheet: -0.41 (0.56), residues: 75 loop : -1.29 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 317 HIS 0.003 0.001 HIS A 67 PHE 0.017 0.001 PHE A 316 TYR 0.009 0.001 TYR A 852 ARG 0.002 0.000 ARG A 969 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4441.35 seconds wall clock time: 79 minutes 38.92 seconds (4778.92 seconds total)