Starting phenix.real_space_refine on Fri Oct 23 22:33:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vto_65337/10_2026/9vto_65337.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vto_65337/10_2026/9vto_65337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vto_65337/10_2026/9vto_65337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vto_65337/10_2026/9vto_65337.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vto_65337/10_2026/9vto_65337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vto_65337/10_2026/9vto_65337.map" } resolution = 2.41 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= 0.018 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 63 5.16 5 C 7061 2.51 5 N 1834 2.21 5 O 2008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10973 Number of models: 1 Model: "" Number of chains: 2 Chain: "Aa" Number of atoms: 10909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1361, 10909 Classifications: {'peptide': 1361} Link IDs: {'PTRANS': 57, 'TRANS': 1303} Chain breaks: 4 Chain: "Aa" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 1, 'ANP': 2} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Time building chain proxies: 2.54, per 1000 atoms: 0.23 Number of scatterers: 10973 At special positions: 0 Unit cell: (80.636, 101.856, 143.235, 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 63 16.00 P 6 15.00 Mg 1 11.99 O 2008 8.00 N 1834 7.00 C 7061 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: 0.70 Conformation dependent library (CDL) restraints added in 488.9 milliseconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 7 sheets defined 60.9% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'Aa' and resid 86 through 90 Processing helix chain 'Aa' and resid 97 through 112 Processing helix chain 'Aa' and resid 112 through 117 Processing helix chain 'Aa' and resid 145 through 157 Processing helix chain 'Aa' and resid 192 through 201 Processing helix chain 'Aa' and resid 221 through 229 Processing helix chain 'Aa' and resid 247 through 259 Processing helix chain 'Aa' and resid 261 through 265 removed outlier: 3.662A pdb=" N ARGAa 264 " --> pdb=" O PROAa 261 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLYAa 265 " --> pdb=" O GLNAa 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aa' and resid 261 through 265' Processing helix chain 'Aa' and resid 269 through 285 Processing helix chain 'Aa' and resid 287 through 291 Processing helix chain 'Aa' and resid 304 through 319 removed outlier: 3.799A pdb=" N SERAa 319 " --> pdb=" O GLUAa 315 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 334 through 353 Processing helix chain 'Aa' and resid 364 through 370 removed outlier: 3.645A pdb=" N LEUAa 370 " --> pdb=" O ASPAa 366 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 390 through 399 Processing helix chain 'Aa' and resid 407 through 415 Processing helix chain 'Aa' and resid 434 through 444 Processing helix chain 'Aa' and resid 445 through 464 removed outlier: 3.724A pdb=" N GLUAa 463 " --> pdb=" O PHEAa 459 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARGAa 464 " --> pdb=" O VALAa 460 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 467 through 479 removed outlier: 3.610A pdb=" N LYSAa 478 " --> pdb=" O SERAa 474 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 492 through 511 Processing helix chain 'Aa' and resid 512 through 533 removed outlier: 3.623A pdb=" N VALAa 532 " --> pdb=" O ILEAa 528 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHEAa 533 " --> pdb=" O LEUAa 529 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 539 through 541 No H-bonds generated for 'chain 'Aa' and resid 539 through 541' Processing helix chain 'Aa' and resid 542 through 563 removed outlier: 3.549A pdb=" N LEUAa 563 " --> pdb=" O PHEAa 559 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 564 through 568 Processing helix chain 'Aa' and resid 571 through 581 Processing helix chain 'Aa' and resid 585 through 597 Processing helix chain 'Aa' and resid 597 through 617 removed outlier: 3.585A pdb=" N PHEAa 610 " --> pdb=" O METAa 606 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VALAa 611 " --> pdb=" O SERAa 607 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASNAa 617 " --> pdb=" O TYRAa 613 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 621 through 650 Processing helix chain 'Aa' and resid 652 through 670 removed outlier: 3.948A pdb=" N THRAa 658 " --> pdb=" O SERAa 654 " (cutoff:3.500A) Proline residue: Aa 659 - end of helix Processing helix chain 'Aa' and resid 685 through 690 removed outlier: 3.548A pdb=" N TYRAa 689 " --> pdb=" O ARGAa 685 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 691 through 706 removed outlier: 3.789A pdb=" N TYRAa 695 " --> pdb=" O ASNAa 691 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 726 through 730 Processing helix chain 'Aa' and resid 746 through 754 Processing helix chain 'Aa' and resid 757 through 759 No H-bonds generated for 'chain 'Aa' and resid 757 through 759' Processing helix chain 'Aa' and resid 760 through 785 removed outlier: 3.827A pdb=" N LEUAa 765 " --> pdb=" O LYSAa 761 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLUAa 784 " --> pdb=" O ILEAa 780 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHEAa 785 " --> pdb=" O ALAAa 781 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 799 through 806 removed outlier: 3.696A pdb=" N LEUAa 803 " --> pdb=" O LYSAa 800 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LYSAa 804 " --> pdb=" O GLYAa 801 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYSAa 805 " --> pdb=" O SERAa 802 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 900 through 909 Processing helix chain 'Aa' and resid 932 through 937 Processing helix chain 'Aa' and resid 951 through 964 Processing helix chain 'Aa' and resid 969 through 984 Processing helix chain 'Aa' and resid 986 through 990 removed outlier: 3.833A pdb=" N ALAAa 990 " --> pdb=" O THRAa 987 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1002 through 1017 removed outlier: 3.519A pdb=" N ARGAa1008 " --> pdb=" O GLUAa1004 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLUAa1014 " --> pdb=" O THRAa1010 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALAAa1017 " --> pdb=" O VALAa1013 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1033 through 1050 Processing helix chain 'Aa' and resid 1062 through 1067 Processing helix chain 'Aa' and resid 1088 through 1090 No H-bonds generated for 'chain 'Aa' and resid 1088 through 1090' Processing helix chain 'Aa' and resid 1091 through 1101 Processing helix chain 'Aa' and resid 1111 through 1120 removed outlier: 3.700A pdb=" N LEUAa1117 " --> pdb=" O ALAAa1113 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1131 through 1138 Processing helix chain 'Aa' and resid 1139 through 1157 removed outlier: 3.579A pdb=" N SERAa1157 " --> pdb=" O GLUAa1153 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1164 through 1169 removed outlier: 3.520A pdb=" N LEUAa1169 " --> pdb=" O GLUAa1166 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1174 through 1192 Processing helix chain 'Aa' and resid 1193 through 1215 Processing helix chain 'Aa' and resid 1221 through 1235 removed outlier: 3.633A pdb=" N GLNAa1226 " --> pdb=" O METAa1222 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1238 through 1260 Proline residue: Aa1248 - end of helix Processing helix chain 'Aa' and resid 1268 through 1300 removed outlier: 3.627A pdb=" N GLUAa1280 " --> pdb=" O GLNAa1276 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILEAa1281 " --> pdb=" O ILEAa1277 " (cutoff:3.500A) Proline residue: Aa1282 - end of helix removed outlier: 4.109A pdb=" N TYRAa1297 " --> pdb=" O PHEAa1293 " (cutoff:3.500A) Proline residue: Aa1298 - end of helix Processing helix chain 'Aa' and resid 1301 through 1304 Processing helix chain 'Aa' and resid 1312 through 1338 removed outlier: 4.155A pdb=" N VALAa1316 " --> pdb=" O ASNAa1312 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1342 through 1360 Processing helix chain 'Aa' and resid 1374 through 1380 Processing helix chain 'Aa' and resid 1381 through 1395 removed outlier: 3.683A pdb=" N TYRAa1385 " --> pdb=" O ASNAa1381 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SERAa1392 " --> pdb=" O GLNAa1388 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1417 through 1430 removed outlier: 3.555A pdb=" N TYRAa1421 " --> pdb=" O SERAa1417 " (cutoff:3.500A) Proline residue: Aa1424 - end of helix Processing helix chain 'Aa' and resid 1448 through 1456 removed outlier: 4.105A pdb=" N PHEAa1452 " --> pdb=" O SERAa1448 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1462 through 1490 removed outlier: 3.691A pdb=" N VALAa1490 " --> pdb=" O TRPAa1486 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Aa' and resid 166 through 177 removed outlier: 5.682A pdb=" N PHEAa 167 " --> pdb=" O VALAa 133 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VALAa 133 " --> pdb=" O PHEAa 167 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILEAa 169 " --> pdb=" O TYRAa 131 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYRAa 131 " --> pdb=" O ILEAa 169 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYSAa 171 " --> pdb=" O ARGAa 129 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARGAa 129 " --> pdb=" O LYSAa 171 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N METAa 173 " --> pdb=" O ASNAa 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Aa' and resid 166 through 177 removed outlier: 5.682A pdb=" N PHEAa 167 " --> pdb=" O VALAa 133 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VALAa 133 " --> pdb=" O PHEAa 167 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILEAa 169 " --> pdb=" O TYRAa 131 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYRAa 131 " --> pdb=" O ILEAa 169 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYSAa 171 " --> pdb=" O ARGAa 129 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARGAa 129 " --> pdb=" O LYSAa 171 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N METAa 173 " --> pdb=" O ASNAa 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Aa' and resid 233 through 236 removed outlier: 6.824A pdb=" N ILEAa 234 " --> pdb=" O CYSAa 325 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASPAa 327 " --> pdb=" O ILEAa 234 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SERAa 236 " --> pdb=" O ASPAa 327 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLNAa 324 " --> pdb=" O LEUAa 357 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALAAa 359 " --> pdb=" O GLNAa 324 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TRPAa 326 " --> pdb=" O ALAAa 359 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHEAa 384 " --> pdb=" O VALAa 376 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYRAa 378 " --> pdb=" O GLNAa 382 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLNAa 382 " --> pdb=" O TYRAa 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Aa' and resid 709 through 711 Processing sheet with id=AA5, first strand: chain 'Aa' and resid 874 through 885 removed outlier: 6.980A pdb=" N ARGAa 875 " --> pdb=" O LYSAa 869 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LYSAa 869 " --> pdb=" O ARGAa 875 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILEAa 877 " --> pdb=" O GLNAa 867 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLNAa 867 " --> pdb=" O ILEAa 877 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASPAa 879 " --> pdb=" O THRAa 865 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THRAa 865 " --> pdb=" O ASPAa 879 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N VALAa 881 " --> pdb=" O ASPAa 863 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHEAa 859 " --> pdb=" O VALAa 885 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEUAa 864 " --> pdb=" O ASPAa 919 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASPAa 919 " --> pdb=" O LEUAa 864 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYRAa 866 " --> pdb=" O ILEAa 917 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILEAa 917 " --> pdb=" O TYRAa 866 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Aa' and resid 938 through 940 removed outlier: 6.230A pdb=" N GLYAa 938 " --> pdb=" O PHEAa1024 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ASPAa1026 " --> pdb=" O GLYAa 938 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VALAa 940 " --> pdb=" O ASPAa1026 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEUAa1023 " --> pdb=" O LEUAa1055 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THRAa1057 " --> pdb=" O LEUAa1023 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEUAa1025 " --> pdb=" O THRAa1057 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILEAa 890 " --> pdb=" O ARGAa1071 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEUAa1073 " --> pdb=" O ILEAa 890 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALAAa 892 " --> pdb=" O LEUAa1073 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEUAa1075 " --> pdb=" O ALAAa 892 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N METAa 894 " --> pdb=" O LEUAa1075 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYRAa1083 " --> pdb=" O PHEAa1074 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLNAa1076 " --> pdb=" O THRAa1081 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N THRAa1081 " --> pdb=" O GLNAa1076 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Aa' and resid 1408 through 1409 585 hydrogen bonds defined for protein. 1692 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: 1.67 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2763 1.33 - 1.45: 2453 1.45 - 1.57: 5938 1.57 - 1.70: 2 1.70 - 1.82: 103 Bond restraints: 11259 Sorted by residual: bond pdb=" N3B ANPAa1603 " pdb=" PG ANPAa1603 " ideal model delta sigma weight residual 1.795 1.529 0.266 2.00e-02 2.50e+03 1.78e+02 bond pdb=" N3B ANPAa1602 " pdb=" PG ANPAa1602 " ideal model delta sigma weight residual 1.795 1.564 0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" O3A ANPAa1603 " pdb=" PB ANPAa1603 " ideal model delta sigma weight residual 1.700 1.532 0.168 2.00e-02 2.50e+03 7.03e+01 bond pdb=" O3A ANPAa1602 " pdb=" PB ANPAa1602 " ideal model delta sigma weight residual 1.700 1.536 0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" N3B ANPAa1603 " pdb=" PB ANPAa1603 " ideal model delta sigma weight residual 1.669 1.553 0.116 2.00e-02 2.50e+03 3.36e+01 ... (remaining 11254 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 15016 2.64 - 5.29: 224 5.29 - 7.93: 21 7.93 - 10.58: 9 10.58 - 13.22: 3 Bond angle restraints: 15273 Sorted by residual: angle pdb=" OE1 GLNAa 942 " pdb=" CD GLNAa 942 " pdb=" NE2 GLNAa 942 " ideal model delta sigma weight residual 122.60 116.79 5.81 1.00e+00 1.00e+00 3.38e+01 angle pdb=" N3B ANPAa1603 " pdb=" PG ANPAa1603 " pdb=" O1G ANPAa1603 " ideal model delta sigma weight residual 106.28 119.50 -13.22 3.00e+00 1.11e-01 1.94e+01 angle pdb=" O1A ANPAa1603 " pdb=" PA ANPAa1603 " pdb=" O2A ANPAa1603 " ideal model delta sigma weight residual 120.18 107.18 13.00 3.00e+00 1.11e-01 1.88e+01 angle pdb=" CB HISAa 242 " pdb=" CG HISAa 242 " pdb=" CD2 HISAa 242 " ideal model delta sigma weight residual 131.20 125.84 5.36 1.30e+00 5.92e-01 1.70e+01 angle pdb=" C ILEAa1058 " pdb=" CA ILEAa1058 " pdb=" CB ILEAa1058 " ideal model delta sigma weight residual 110.33 116.30 -5.97 1.46e+00 4.69e-01 1.67e+01 ... (remaining 15268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.65: 6362 31.65 - 63.31: 247 63.31 - 94.96: 42 94.96 - 126.62: 0 126.62 - 158.27: 1 Dihedral angle restraints: 6652 sinusoidal: 2679 harmonic: 3973 Sorted by residual: dihedral pdb=" O1B ANPAa1603 " pdb=" N3B ANPAa1603 " pdb=" PB ANPAa1603 " pdb=" PG ANPAa1603 " ideal model delta sinusoidal sigma weight residual 35.15 -123.12 158.27 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" CA ALAAa 201 " pdb=" C ALAAa 201 " pdb=" N VALAa 202 " pdb=" CA VALAa 202 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA VALAa 716 " pdb=" C VALAa 716 " pdb=" N PROAa 717 " pdb=" CA PROAa 717 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 6649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1531 0.084 - 0.169: 102 0.169 - 0.253: 4 0.253 - 0.338: 2 0.338 - 0.422: 2 Chirality restraints: 1641 Sorted by residual: chirality pdb=" C3' ANPAa1603 " pdb=" C2' ANPAa1603 " pdb=" C4' ANPAa1603 " pdb=" O3' ANPAa1603 " both_signs ideal model delta sigma weight residual False -2.36 -2.78 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" C3' ANPAa1602 " pdb=" C2' ANPAa1602 " pdb=" C4' ANPAa1602 " pdb=" O3' ANPAa1602 " both_signs ideal model delta sigma weight residual False -2.36 -2.73 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C2' ANPAa1602 " pdb=" C1' ANPAa1602 " pdb=" C3' ANPAa1602 " pdb=" O2' ANPAa1602 " both_signs ideal model delta sigma weight residual False -2.72 -2.43 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1638 not shown) Planarity restraints: 1940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYRAa 939 " -0.050 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYRAa 939 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYRAa 939 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYRAa 939 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 TYRAa 939 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYRAa 939 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYRAa 939 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYRAa 939 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANPAa1602 " -0.047 2.00e-02 2.50e+03 2.45e-02 1.65e+01 pdb=" C2 ANPAa1602 " 0.024 2.00e-02 2.50e+03 pdb=" C4 ANPAa1602 " -0.000 2.00e-02 2.50e+03 pdb=" C5 ANPAa1602 " -0.016 2.00e-02 2.50e+03 pdb=" C6 ANPAa1602 " -0.014 2.00e-02 2.50e+03 pdb=" C8 ANPAa1602 " 0.049 2.00e-02 2.50e+03 pdb=" N1 ANPAa1602 " 0.002 2.00e-02 2.50e+03 pdb=" N3 ANPAa1602 " 0.016 2.00e-02 2.50e+03 pdb=" N6 ANPAa1602 " -0.023 2.00e-02 2.50e+03 pdb=" N7 ANPAa1602 " 0.009 2.00e-02 2.50e+03 pdb=" N9 ANPAa1602 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRAa 866 " -0.035 2.00e-02 2.50e+03 2.61e-02 1.36e+01 pdb=" CG TYRAa 866 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYRAa 866 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYRAa 866 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYRAa 866 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYRAa 866 " 0.033 2.00e-02 2.50e+03 pdb=" CZ TYRAa 866 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYRAa 866 " -0.048 2.00e-02 2.50e+03 ... (remaining 1937 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 44 2.45 - 3.06: 7019 3.06 - 3.68: 17245 3.68 - 4.29: 27201 4.29 - 4.90: 43646 Nonbonded interactions: 95155 Sorted by model distance: nonbonded pdb="MG MGAa1601 " pdb=" O2G ANPAa1602 " model vdw 1.839 2.170 nonbonded pdb=" OG1 THRAa 902 " pdb="MG MGAa1601 " model vdw 2.012 2.170 nonbonded pdb=" OE1 GLNAa 942 " pdb="MG MGAa1601 " model vdw 2.038 2.170 nonbonded pdb="MG MGAa1601 " pdb=" O2B ANPAa1602 " model vdw 2.126 2.170 nonbonded pdb=" O GLNAa1388 " pdb=" OG SERAa1392 " model vdw 2.206 3.040 ... (remaining 95150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.130 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.006 0.266 11259 Z= 0.318 Angle : 0.725 13.221 15273 Z= 0.396 Chirality : 0.045 0.422 1641 Planarity : 0.005 0.065 1940 Dihedral : 17.050 158.271 4108 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.86 % Allowed : 14.41 % Favored : 84.73 % 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: 1.13 (0.23), residues: 1351 helix: 1.22 (0.18), residues: 745 sheet: -0.16 (0.57), residues: 79 loop : 0.41 (0.29), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAa1146 TYR 0.050 0.002 TYRAa 939 PHE 0.019 0.001 PHEAa 243 TRP 0.033 0.002 TRPAa 861 HIS 0.012 0.001 HISAa1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.32 (11259) covalent geometry : angle 0.72542 / 0.40 (15273) hydrogen bonds : bond 0.20650 / 12.76 ( 580) hydrogen bonds : angle 6.69681 / 4.76 ( 1692) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.365 Fit side-chains REVERT: Aa 211 LYS cc_start: 0.7536 (mppt) cc_final: 0.7272 (mptp) REVERT: Aa 615 MET cc_start: 0.8656 (ttm) cc_final: 0.8368 (mtp) REVERT: Aa 971 LYS cc_start: 0.8003 (tmmm) cc_final: 0.7645 (tptp) REVERT: Aa 1004 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7847 (tt0) outliers start: 10 outliers final: 9 residues processed: 167 average time/residue: 0.5958 time to fit residues: 107.0758 Evaluate side-chains 160 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 202 VAL Chi-restraints excluded: chain Aa residue 431 VAL Chi-restraints excluded: chain Aa residue 439 GLU Chi-restraints excluded: chain Aa residue 554 VAL Chi-restraints excluded: chain Aa residue 921 GLU Chi-restraints excluded: chain Aa residue 993 LEU Chi-restraints excluded: chain Aa residue 1287 VAL Chi-restraints excluded: chain Aa residue 1369 VAL Chi-restraints excluded: chain Aa residue 1455 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 0.0060 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0040 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 104 ASN Aa 135 ASN Aa 263 ASN ** Aa 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1052 GLN Aa1076 GLN Aa1090 ASN Aa1111 ASN Aa1118 GLN Aa1143 GLN Aa1245 GLN Aa1284 GLN Aa1303 ASN Aa1388 GLN Aa1414 ASN Aa1445 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112758 restraints weight = 12392.211| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.65 r_work: 0.3206 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11259 Z= 0.121 Angle : 0.501 5.645 15273 Z= 0.262 Chirality : 0.041 0.152 1641 Planarity : 0.004 0.047 1940 Dihedral : 10.481 163.771 1578 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.40 % Allowed : 12.86 % Favored : 84.73 % 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: 1.66 (0.23), residues: 1351 helix: 1.82 (0.19), residues: 742 sheet: -0.28 (0.59), residues: 70 loop : 0.40 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAa1146 TYR 0.014 0.001 TYRAa1425 PHE 0.013 0.001 PHEAa1233 TRP 0.008 0.001 TRPAa 442 HIS 0.003 0.001 HISAa1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (11259) covalent geometry : angle 0.50112 / 0.26 (15273) hydrogen bonds : bond 0.04782 / 3.11 ( 580) hydrogen bonds : angle 4.63835 / 3.29 ( 1692) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.413 Fit side-chains REVERT: Aa 88 GLN cc_start: 0.8022 (mt0) cc_final: 0.7796 (mt0) REVERT: Aa 211 LYS cc_start: 0.7476 (mppt) cc_final: 0.7167 (mptt) REVERT: Aa 472 ARG cc_start: 0.7821 (ttm170) cc_final: 0.7611 (tpp80) REVERT: Aa 550 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7487 (mpp) REVERT: Aa 921 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7626 (tp30) REVERT: Aa 971 LYS cc_start: 0.8072 (tmmm) cc_final: 0.7729 (tptp) REVERT: Aa 988 ASP cc_start: 0.8612 (m-30) cc_final: 0.8321 (p0) REVERT: Aa 1004 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8053 (tt0) REVERT: Aa 1147 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8172 (mm-30) REVERT: Aa 1222 MET cc_start: 0.6822 (mpt) cc_final: 0.4422 (tmm) REVERT: Aa 1446 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7277 (pmm) outliers start: 28 outliers final: 11 residues processed: 188 average time/residue: 0.5693 time to fit residues: 115.7133 Evaluate side-chains 170 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 157 HIS Chi-restraints excluded: chain Aa residue 431 VAL Chi-restraints excluded: chain Aa residue 439 GLU Chi-restraints excluded: chain Aa residue 467 THR Chi-restraints excluded: chain Aa residue 550 MET Chi-restraints excluded: chain Aa residue 606 MET Chi-restraints excluded: chain Aa residue 663 LEU Chi-restraints excluded: chain Aa residue 671 THR Chi-restraints excluded: chain Aa residue 993 LEU Chi-restraints excluded: chain Aa residue 1221 ASN Chi-restraints excluded: chain Aa residue 1287 VAL Chi-restraints excluded: chain Aa residue 1369 VAL Chi-restraints excluded: chain Aa residue 1446 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [70, 72, 22, 4, 65, 23, 27, 60, 82, 58, 42] chunk 70 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 135 ASN ** Aa 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1118 GLN Aa1143 GLN Aa1388 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.134649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107587 restraints weight = 12484.973| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.65 r_work: 0.3132 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 11259 Z= 0.233 Angle : 0.589 7.359 15273 Z= 0.309 Chirality : 0.045 0.205 1641 Planarity : 0.005 0.051 1940 Dihedral : 10.270 161.925 1572 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.57 % Allowed : 13.64 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.23), residues: 1351 helix: 1.52 (0.18), residues: 752 sheet: -0.64 (0.51), residues: 79 loop : 0.40 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAa 126 TYR 0.019 0.002 TYRAa1249 PHE 0.016 0.002 PHEAa 625 TRP 0.011 0.002 TRPAa 442 HIS 0.005 0.001 HISAa1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.23 (11259) covalent geometry : angle 0.58908 / 0.31 (15273) hydrogen bonds : bond 0.05320 / 3.44 ( 580) hydrogen bonds : angle 4.61690 / 3.30 ( 1692) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.409 Fit side-chains REVERT: Aa 106 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.5323 (ttm-80) REVERT: Aa 211 LYS cc_start: 0.7652 (mppt) cc_final: 0.7312 (mppt) REVERT: Aa 550 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.7477 (mpp) REVERT: Aa 615 MET cc_start: 0.8800 (ttm) cc_final: 0.8501 (mtp) REVERT: Aa 803 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8251 (mp) REVERT: Aa 921 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7532 (tp30) REVERT: Aa 1004 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8166 (tt0) REVERT: Aa 1034 SER cc_start: 0.8651 (p) cc_final: 0.8375 (m) outliers start: 30 outliers final: 16 residues processed: 181 average time/residue: 0.5438 time to fit residues: 106.7237 Evaluate side-chains 170 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 106 ARG Chi-restraints excluded: chain Aa residue 280 VAL Chi-restraints excluded: chain Aa residue 354 THR Chi-restraints excluded: chain Aa residue 431 VAL Chi-restraints excluded: chain Aa residue 439 GLU Chi-restraints excluded: chain Aa residue 467 THR Chi-restraints excluded: chain Aa residue 550 MET Chi-restraints excluded: chain Aa residue 554 VAL Chi-restraints excluded: chain Aa residue 606 MET Chi-restraints excluded: chain Aa residue 611 VAL Chi-restraints excluded: chain Aa residue 663 LEU Chi-restraints excluded: chain Aa residue 671 THR Chi-restraints excluded: chain Aa residue 803 LEU Chi-restraints excluded: chain Aa residue 913 THR Chi-restraints excluded: chain Aa residue 1204 VAL Chi-restraints excluded: chain Aa residue 1287 VAL Chi-restraints excluded: chain Aa residue 1369 VAL Chi-restraints excluded: chain Aa residue 1395 LEU Chi-restraints excluded: chain Aa residue 1400 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [28, 29, 59, 57, 8, 26, 80, 14, 100, 75, 78] chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 135 ASN ** Aa 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1118 GLN Aa1143 GLN ** Aa1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109019 restraints weight = 12459.989| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.65 r_work: 0.3155 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11259 Z= 0.166 Angle : 0.539 6.712 15273 Z= 0.280 Chirality : 0.042 0.151 1641 Planarity : 0.004 0.049 1940 Dihedral : 9.626 159.070 1570 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.32 % Allowed : 14.49 % Favored : 83.19 % 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: 1.41 (0.23), residues: 1351 helix: 1.60 (0.18), residues: 753 sheet: -0.73 (0.50), residues: 79 loop : 0.37 (0.29), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAa 126 TYR 0.015 0.002 TYRAa1385 PHE 0.014 0.001 PHEAa1233 TRP 0.010 0.001 TRPAa 634 HIS 0.003 0.001 HISAa 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (11259) covalent geometry : angle 0.53924 / 0.28 (15273) hydrogen bonds : bond 0.04628 / 3.01 ( 580) hydrogen bonds : angle 4.43752 / 3.16 ( 1692) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.429 Fit side-chains REVERT: Aa 157 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.7304 (t-90) REVERT: Aa 211 LYS cc_start: 0.7588 (mppt) cc_final: 0.7249 (mppt) REVERT: Aa 550 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.7544 (mpp) REVERT: Aa 615 MET cc_start: 0.8796 (ttm) cc_final: 0.8479 (mtp) REVERT: Aa 803 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8273 (mp) REVERT: Aa 971 LYS cc_start: 0.8097 (tmmm) cc_final: 0.7758 (tptp) REVERT: Aa 1004 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8124 (tt0) REVERT: Aa 1198 TYR cc_start: 0.8805 (m-80) cc_final: 0.8594 (m-80) REVERT: Aa 1432 TYR cc_start: 0.7661 (p90) cc_final: 0.7436 (p90) outliers start: 27 outliers final: 16 residues processed: 176 average time/residue: 0.5516 time to fit residues: 105.3429 Evaluate side-chains 172 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 157 HIS Chi-restraints excluded: chain Aa residue 280 VAL Chi-restraints excluded: chain Aa residue 413 THR Chi-restraints excluded: chain Aa residue 431 VAL Chi-restraints excluded: chain Aa residue 439 GLU Chi-restraints excluded: chain Aa residue 467 THR Chi-restraints excluded: chain Aa residue 550 MET Chi-restraints excluded: chain Aa residue 554 VAL Chi-restraints excluded: chain Aa residue 606 MET Chi-restraints excluded: chain Aa residue 611 VAL Chi-restraints excluded: chain Aa residue 663 LEU Chi-restraints excluded: chain Aa residue 671 THR Chi-restraints excluded: chain Aa residue 803 LEU Chi-restraints excluded: chain Aa residue 894 MET Chi-restraints excluded: chain Aa residue 1159 LEU Chi-restraints excluded: chain Aa residue 1204 VAL Chi-restraints excluded: chain Aa residue 1287 VAL Chi-restraints excluded: chain Aa residue 1369 VAL Chi-restraints excluded: chain Aa residue 1395 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [14, 43, 3, 109, 93, 54, 5, 15, 106, 4, 58] chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 135 ASN ** Aa 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1118 GLN Aa1143 GLN ** Aa1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1388 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.137170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110375 restraints weight = 12344.394| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.66 r_work: 0.3179 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11259 Z= 0.132 Angle : 0.506 6.711 15273 Z= 0.262 Chirality : 0.041 0.149 1641 Planarity : 0.004 0.047 1940 Dihedral : 8.880 156.477 1570 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.66 % Allowed : 14.67 % Favored : 82.68 % 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: 1.59 (0.23), residues: 1351 helix: 1.78 (0.19), residues: 751 sheet: -0.72 (0.50), residues: 79 loop : 0.40 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGAa 126 TYR 0.013 0.002 TYRAa1421 PHE 0.013 0.001 PHEAa 438 TRP 0.010 0.001 TRPAa 634 HIS 0.003 0.001 HISAa 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11259) covalent geometry : angle 0.50569 / 0.26 (15273) hydrogen bonds : bond 0.04208 / 2.74 ( 580) hydrogen bonds : angle 4.28801 / 3.05 ( 1692) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.298 Fit side-chains REVERT: Aa 106 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.5436 (ttm-80) REVERT: Aa 157 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.7297 (t-90) REVERT: Aa 177 MET cc_start: 0.8860 (mpt) cc_final: 0.8445 (mpt) REVERT: Aa 211 LYS cc_start: 0.7580 (mppt) cc_final: 0.7260 (mppt) REVERT: Aa 550 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.7536 (mpp) REVERT: Aa 615 MET cc_start: 0.8802 (ttm) cc_final: 0.8478 (mtp) REVERT: Aa 803 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8207 (mt) REVERT: Aa 894 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8883 (mtp) REVERT: Aa 971 LYS cc_start: 0.8105 (tmmm) cc_final: 0.7762 (tptp) REVERT: Aa 1004 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8048 (tt0) REVERT: Aa 1432 TYR cc_start: 0.7686 (p90) cc_final: 0.7412 (p90) outliers start: 31 outliers final: 15 residues processed: 176 average time/residue: 0.5338 time to fit residues: 102.0637 Evaluate side-chains 173 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 106 ARG Chi-restraints excluded: chain Aa residue 157 HIS Chi-restraints excluded: chain Aa residue 280 VAL Chi-restraints excluded: chain Aa residue 413 THR Chi-restraints excluded: chain Aa residue 431 VAL Chi-restraints excluded: chain Aa residue 439 GLU Chi-restraints excluded: chain Aa residue 467 THR Chi-restraints excluded: chain Aa residue 550 MET Chi-restraints excluded: chain Aa residue 554 VAL Chi-restraints excluded: chain Aa residue 611 VAL Chi-restraints excluded: chain Aa residue 663 LEU Chi-restraints excluded: chain Aa residue 671 THR Chi-restraints excluded: chain Aa residue 803 LEU Chi-restraints excluded: chain Aa residue 894 MET Chi-restraints excluded: chain Aa residue 993 LEU Chi-restraints excluded: chain Aa residue 1159 LEU Chi-restraints excluded: chain Aa residue 1204 VAL Chi-restraints excluded: chain Aa residue 1221 ASN Chi-restraints excluded: chain Aa residue 1287 VAL Chi-restraints excluded: chain Aa residue 1369 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [116, 61, 106, 135, 17, 117, 6, 75, 118, 10, 90] chunk 116 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 75 optimal weight: 0.0470 chunk 118 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 135 ASN ** Aa 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1118 GLN Aa1143 GLN ** Aa1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1388 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111511 restraints weight = 12433.068| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.66 r_work: 0.3194 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11259 Z= 0.115 Angle : 0.489 7.394 15273 Z= 0.254 Chirality : 0.040 0.148 1641 Planarity : 0.004 0.046 1940 Dihedral : 8.411 155.762 1570 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.32 % Allowed : 15.18 % Favored : 82.50 % 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: 1.73 (0.23), residues: 1351 helix: 1.98 (0.19), residues: 744 sheet: -0.71 (0.52), residues: 79 loop : 0.36 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAa 126 TYR 0.015 0.002 TYRAa1421 PHE 0.014 0.001 PHEAa1233 TRP 0.010 0.001 TRPAa 634 HIS 0.002 0.001 HISAa 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (11259) covalent geometry : angle 0.48934 / 0.25 (15273) hydrogen bonds : bond 0.03970 / 2.59 ( 580) hydrogen bonds : angle 4.19210 / 2.98 ( 1692) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.262 Fit side-chains REVERT: Aa 106 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.5493 (ttm-80) REVERT: Aa 157 HIS cc_start: 0.7580 (OUTLIER) cc_final: 0.7304 (t-90) REVERT: Aa 177 MET cc_start: 0.8850 (mpt) cc_final: 0.8466 (mpt) REVERT: Aa 211 LYS cc_start: 0.7547 (mppt) cc_final: 0.7247 (mppt) REVERT: Aa 550 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.7608 (mpp) REVERT: Aa 615 MET cc_start: 0.8761 (ttm) cc_final: 0.8430 (mtp) REVERT: Aa 803 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8224 (mt) REVERT: Aa 971 LYS cc_start: 0.8104 (tmmm) cc_final: 0.7756 (tptp) REVERT: Aa 1004 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8043 (tt0) REVERT: Aa 1432 TYR cc_start: 0.7609 (p90) cc_final: 0.7324 (p90) outliers start: 27 outliers final: 13 residues processed: 177 average time/residue: 0.5581 time to fit residues: 106.6741 Evaluate side-chains 167 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 106 ARG Chi-restraints excluded: chain Aa residue 157 HIS Chi-restraints excluded: chain Aa residue 413 THR Chi-restraints excluded: chain Aa residue 431 VAL Chi-restraints excluded: chain Aa residue 439 GLU Chi-restraints excluded: chain Aa residue 467 THR Chi-restraints excluded: chain Aa residue 550 MET Chi-restraints excluded: chain Aa residue 554 VAL Chi-restraints excluded: chain Aa residue 663 LEU Chi-restraints excluded: chain Aa residue 671 THR Chi-restraints excluded: chain Aa residue 803 LEU Chi-restraints excluded: chain Aa residue 993 LEU Chi-restraints excluded: chain Aa residue 1159 LEU Chi-restraints excluded: chain Aa residue 1204 VAL Chi-restraints excluded: chain Aa residue 1221 ASN Chi-restraints excluded: chain Aa residue 1287 VAL Chi-restraints excluded: chain Aa residue 1369 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [99, 13, 45, 108, 42, 80, 34, 116, 0, 100, 89] chunk 99 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 116 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 135 ASN ** Aa 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1118 GLN Aa1143 GLN ** Aa1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1388 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.138561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112009 restraints weight = 12383.572| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.66 r_work: 0.3200 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11259 Z= 0.115 Angle : 0.496 9.718 15273 Z= 0.257 Chirality : 0.040 0.147 1641 Planarity : 0.004 0.046 1940 Dihedral : 8.189 155.567 1570 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.14 % Allowed : 15.95 % Favored : 81.90 % 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: 1.80 (0.23), residues: 1351 helix: 2.02 (0.19), residues: 746 sheet: -0.71 (0.52), residues: 79 loop : 0.41 (0.30), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAa 126 TYR 0.017 0.002 TYRAa 427 PHE 0.012 0.001 PHEAa 438 TRP 0.010 0.001 TRPAa 634 HIS 0.002 0.001 HISAa1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (11259) covalent geometry : angle 0.49630 / 0.26 (15273) hydrogen bonds : bond 0.03888 / 2.53 ( 580) hydrogen bonds : angle 4.14957 / 2.95 ( 1692) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.431 Fit side-chains REVERT: Aa 106 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.5568 (ttm-80) REVERT: Aa 157 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7307 (t-90) REVERT: Aa 177 MET cc_start: 0.8848 (mpt) cc_final: 0.8487 (mpt) REVERT: Aa 211 LYS cc_start: 0.7541 (mppt) cc_final: 0.7251 (mppt) REVERT: Aa 550 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7561 (mpp) REVERT: Aa 615 MET cc_start: 0.8752 (ttm) cc_final: 0.8379 (mtp) REVERT: Aa 792 LYS cc_start: 0.8399 (mtpm) cc_final: 0.8184 (mtmm) REVERT: Aa 803 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8259 (mt) REVERT: Aa 971 LYS cc_start: 0.8087 (tmmm) cc_final: 0.7750 (tptp) REVERT: Aa 988 ASP cc_start: 0.8639 (m-30) cc_final: 0.8331 (p0) REVERT: Aa 1004 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8078 (tt0) REVERT: Aa 1432 TYR cc_start: 0.7615 (p90) cc_final: 0.7300 (p90) outliers start: 25 outliers final: 16 residues processed: 177 average time/residue: 0.5606 time to fit residues: 107.4859 Evaluate side-chains 167 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 105 LEU Chi-restraints excluded: chain Aa residue 106 ARG Chi-restraints excluded: chain Aa residue 157 HIS Chi-restraints excluded: chain Aa residue 413 THR Chi-restraints excluded: chain Aa residue 431 VAL Chi-restraints excluded: chain Aa residue 439 GLU Chi-restraints excluded: chain Aa residue 467 THR Chi-restraints excluded: chain Aa residue 550 MET Chi-restraints excluded: chain Aa residue 554 VAL Chi-restraints excluded: chain Aa residue 611 VAL Chi-restraints excluded: chain Aa residue 663 LEU Chi-restraints excluded: chain Aa residue 671 THR Chi-restraints excluded: chain Aa residue 803 LEU Chi-restraints excluded: chain Aa residue 993 LEU Chi-restraints excluded: chain Aa residue 1159 LEU Chi-restraints excluded: chain Aa residue 1204 VAL Chi-restraints excluded: chain Aa residue 1221 ASN Chi-restraints excluded: chain Aa residue 1287 VAL Chi-restraints excluded: chain Aa residue 1369 VAL Chi-restraints excluded: chain Aa residue 1476 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [72, 86, 63, 30, 125, 96, 24, 99, 53, 81, 59] chunk 72 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 135 ASN Aa 925 ASN Aa1118 GLN Aa1143 GLN ** Aa1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1388 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.138818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112402 restraints weight = 12342.974| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.65 r_work: 0.3206 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11259 Z= 0.113 Angle : 0.498 9.115 15273 Z= 0.259 Chirality : 0.040 0.147 1641 Planarity : 0.004 0.044 1940 Dihedral : 8.079 155.484 1570 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.97 % Allowed : 16.47 % Favored : 81.56 % 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: 1.85 (0.23), residues: 1351 helix: 2.07 (0.19), residues: 746 sheet: -0.74 (0.52), residues: 79 loop : 0.42 (0.30), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAa 126 TYR 0.016 0.001 TYRAa 427 PHE 0.013 0.001 PHEAa 438 TRP 0.009 0.001 TRPAa 634 HIS 0.002 0.001 HISAa1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (11259) covalent geometry : angle 0.49807 / 0.26 (15273) hydrogen bonds : bond 0.03815 / 2.49 ( 580) hydrogen bonds : angle 4.09819 / 2.91 ( 1692) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.344 Fit side-chains REVERT: Aa 106 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.5264 (ttm-80) REVERT: Aa 126 ARG cc_start: 0.8394 (ttt90) cc_final: 0.8181 (tpt-90) REVERT: Aa 157 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.7318 (t-170) REVERT: Aa 177 MET cc_start: 0.8846 (mpt) cc_final: 0.8502 (mpt) REVERT: Aa 211 LYS cc_start: 0.7529 (mppt) cc_final: 0.7251 (mppt) REVERT: Aa 550 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7554 (mpp) REVERT: Aa 615 MET cc_start: 0.8711 (ttm) cc_final: 0.8372 (mtp) REVERT: Aa 792 LYS cc_start: 0.8395 (mtpm) cc_final: 0.8183 (mtmm) REVERT: Aa 803 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8296 (mt) REVERT: Aa 971 LYS cc_start: 0.8088 (tmmm) cc_final: 0.7752 (tptp) REVERT: Aa 988 ASP cc_start: 0.8635 (m-30) cc_final: 0.8330 (p0) REVERT: Aa 1004 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8083 (tt0) REVERT: Aa 1252 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7890 (ptpp) REVERT: Aa 1432 TYR cc_start: 0.7540 (p90) cc_final: 0.7219 (p90) outliers start: 23 outliers final: 13 residues processed: 172 average time/residue: 0.5234 time to fit residues: 97.6841 Evaluate side-chains 163 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 106 ARG Chi-restraints excluded: chain Aa residue 157 HIS Chi-restraints excluded: chain Aa residue 431 VAL Chi-restraints excluded: chain Aa residue 439 GLU Chi-restraints excluded: chain Aa residue 467 THR Chi-restraints excluded: chain Aa residue 550 MET Chi-restraints excluded: chain Aa residue 554 VAL Chi-restraints excluded: chain Aa residue 611 VAL Chi-restraints excluded: chain Aa residue 663 LEU Chi-restraints excluded: chain Aa residue 671 THR Chi-restraints excluded: chain Aa residue 803 LEU Chi-restraints excluded: chain Aa residue 993 LEU Chi-restraints excluded: chain Aa residue 1159 LEU Chi-restraints excluded: chain Aa residue 1204 VAL Chi-restraints excluded: chain Aa residue 1287 VAL Chi-restraints excluded: chain Aa residue 1369 VAL Chi-restraints excluded: chain Aa residue 1476 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [122, 95, 111, 32, 11, 128, 18, 67, 0, 53, 66] chunk 122 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 135 ASN Aa1118 GLN Aa1143 GLN Aa1388 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110009 restraints weight = 12338.575| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.63 r_work: 0.3168 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11259 Z= 0.165 Angle : 0.545 8.668 15273 Z= 0.283 Chirality : 0.042 0.142 1641 Planarity : 0.004 0.045 1940 Dihedral : 8.347 157.569 1570 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.97 % Allowed : 16.30 % Favored : 81.73 % 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: 1.66 (0.23), residues: 1351 helix: 1.89 (0.19), residues: 746 sheet: -0.77 (0.51), residues: 79 loop : 0.38 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAa 126 TYR 0.019 0.002 TYRAa 427 PHE 0.014 0.001 PHEAa1216 TRP 0.008 0.001 TRPAa 442 HIS 0.004 0.001 HISAa1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (11259) covalent geometry : angle 0.54538 / 0.28 (15273) hydrogen bonds : bond 0.04401 / 2.86 ( 580) hydrogen bonds : angle 4.25746 / 3.03 ( 1692) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.410 Fit side-chains REVERT: Aa 106 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.5464 (ttm-80) REVERT: Aa 126 ARG cc_start: 0.8344 (ttt90) cc_final: 0.8031 (tpt90) REVERT: Aa 157 HIS cc_start: 0.7574 (OUTLIER) cc_final: 0.7328 (t-170) REVERT: Aa 177 MET cc_start: 0.8911 (mpt) cc_final: 0.8559 (mpt) REVERT: Aa 211 LYS cc_start: 0.7528 (mppt) cc_final: 0.7241 (mppt) REVERT: Aa 550 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.7535 (mpp) REVERT: Aa 615 MET cc_start: 0.8732 (ttm) cc_final: 0.8339 (mtp) REVERT: Aa 792 LYS cc_start: 0.8441 (mtpm) cc_final: 0.8233 (mtmm) REVERT: Aa 803 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8281 (mt) REVERT: Aa 971 LYS cc_start: 0.8077 (tmmm) cc_final: 0.7744 (tptp) REVERT: Aa 988 ASP cc_start: 0.8646 (m-30) cc_final: 0.8322 (p0) REVERT: Aa 1004 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8057 (tt0) REVERT: Aa 1432 TYR cc_start: 0.7517 (p90) cc_final: 0.7190 (p90) outliers start: 23 outliers final: 14 residues processed: 166 average time/residue: 0.5491 time to fit residues: 98.8311 Evaluate side-chains 166 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 106 ARG Chi-restraints excluded: chain Aa residue 157 HIS Chi-restraints excluded: chain Aa residue 280 VAL Chi-restraints excluded: chain Aa residue 431 VAL Chi-restraints excluded: chain Aa residue 439 GLU Chi-restraints excluded: chain Aa residue 467 THR Chi-restraints excluded: chain Aa residue 550 MET Chi-restraints excluded: chain Aa residue 554 VAL Chi-restraints excluded: chain Aa residue 611 VAL Chi-restraints excluded: chain Aa residue 663 LEU Chi-restraints excluded: chain Aa residue 671 THR Chi-restraints excluded: chain Aa residue 733 THR Chi-restraints excluded: chain Aa residue 803 LEU Chi-restraints excluded: chain Aa residue 1159 LEU Chi-restraints excluded: chain Aa residue 1204 VAL Chi-restraints excluded: chain Aa residue 1287 VAL Chi-restraints excluded: chain Aa residue 1369 VAL Chi-restraints excluded: chain Aa residue 1476 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [96, 19, 129, 128, 73, 52, 78, 109, 120, 122, 105] chunk 96 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 135 ASN Aa1118 GLN Aa1143 GLN ** Aa1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1388 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110970 restraints weight = 12347.730| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.64 r_work: 0.3183 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11259 Z= 0.139 Angle : 0.524 9.006 15273 Z= 0.272 Chirality : 0.041 0.144 1641 Planarity : 0.004 0.045 1940 Dihedral : 8.246 157.167 1570 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.80 % Allowed : 16.55 % Favored : 81.65 % 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: 1.69 (0.23), residues: 1351 helix: 1.88 (0.19), residues: 751 sheet: -0.74 (0.52), residues: 79 loop : 0.42 (0.30), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAa 126 TYR 0.018 0.002 TYRAa 427 PHE 0.014 0.001 PHEAa1233 TRP 0.010 0.001 TRPAa 634 HIS 0.004 0.001 HISAa1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (11259) covalent geometry : angle 0.52364 / 0.27 (15273) hydrogen bonds : bond 0.04164 / 2.71 ( 580) hydrogen bonds : angle 4.20306 / 2.98 ( 1692) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.405 Fit side-chains REVERT: Aa 106 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.5582 (ttm-80) REVERT: Aa 157 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.7326 (t-170) REVERT: Aa 177 MET cc_start: 0.8894 (mpt) cc_final: 0.8581 (mpt) REVERT: Aa 211 LYS cc_start: 0.7510 (mppt) cc_final: 0.7232 (mppt) REVERT: Aa 550 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.7549 (mpp) REVERT: Aa 615 MET cc_start: 0.8708 (ttm) cc_final: 0.8363 (mtp) REVERT: Aa 792 LYS cc_start: 0.8428 (mtpm) cc_final: 0.8222 (mtmm) REVERT: Aa 803 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8243 (mt) REVERT: Aa 971 LYS cc_start: 0.8084 (tmmm) cc_final: 0.7749 (tptp) REVERT: Aa 988 ASP cc_start: 0.8646 (m-30) cc_final: 0.8326 (p0) REVERT: Aa 1004 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8049 (tt0) REVERT: Aa 1432 TYR cc_start: 0.7493 (p90) cc_final: 0.7161 (p90) outliers start: 21 outliers final: 15 residues processed: 166 average time/residue: 0.5275 time to fit residues: 95.0447 Evaluate side-chains 166 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 106 ARG Chi-restraints excluded: chain Aa residue 157 HIS Chi-restraints excluded: chain Aa residue 280 VAL Chi-restraints excluded: chain Aa residue 431 VAL Chi-restraints excluded: chain Aa residue 439 GLU Chi-restraints excluded: chain Aa residue 467 THR Chi-restraints excluded: chain Aa residue 550 MET Chi-restraints excluded: chain Aa residue 554 VAL Chi-restraints excluded: chain Aa residue 611 VAL Chi-restraints excluded: chain Aa residue 663 LEU Chi-restraints excluded: chain Aa residue 671 THR Chi-restraints excluded: chain Aa residue 733 THR Chi-restraints excluded: chain Aa residue 803 LEU Chi-restraints excluded: chain Aa residue 1159 LEU Chi-restraints excluded: chain Aa residue 1204 VAL Chi-restraints excluded: chain Aa residue 1221 ASN Chi-restraints excluded: chain Aa residue 1287 VAL Chi-restraints excluded: chain Aa residue 1369 VAL Chi-restraints excluded: chain Aa residue 1476 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [126, 69, 132, 115, 16, 123, 102, 89, 92, 118, 40] chunk 126 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 115 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 135 ASN Aa1118 GLN Aa1143 GLN ** Aa1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1388 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.137691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111227 restraints weight = 12422.844| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.64 r_work: 0.3189 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11259 Z= 0.126 Angle : 0.509 9.001 15273 Z= 0.264 Chirality : 0.041 0.145 1641 Planarity : 0.004 0.044 1940 Dihedral : 8.125 157.142 1570 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.89 % Allowed : 16.55 % Favored : 81.56 % 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: 1.78 (0.23), residues: 1351 helix: 2.00 (0.19), residues: 746 sheet: -0.75 (0.52), residues: 79 loop : 0.42 (0.30), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAa1146 TYR 0.017 0.002 TYRAa 427 PHE 0.015 0.001 PHEAa1233 TRP 0.009 0.001 TRPAa 634 HIS 0.003 0.001 HISAa1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (11259) covalent geometry : angle 0.50860 / 0.26 (15273) hydrogen bonds : bond 0.04010 / 2.61 ( 580) hydrogen bonds : angle 4.16732 / 2.96 ( 1692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4296.70 seconds wall clock time: 73 minutes 55.82 seconds (4435.82 seconds total)