Starting phenix.real_space_refine on Fri Oct 23 16:36:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vtm_65335/10_2026/9vtm_65335.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vtm_65335/10_2026/9vtm_65335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vtm_65335/10_2026/9vtm_65335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vtm_65335/10_2026/9vtm_65335.map" model { file = "/net/cci-nas-00/data/ceres_data/9vtm_65335/10_2026/9vtm_65335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vtm_65335/10_2026/9vtm_65335.cif" } resolution = 2.92 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= -0.001 sd= 0.042 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 62 5.16 5 C 6518 2.51 5 N 1664 2.21 5 O 1835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 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: 10082 Number of models: 1 Model: "" Number of chains: 2 Chain: "Aa" Number of atoms: 10051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 10051 Classifications: {'peptide': 1259} Link IDs: {'PTRANS': 53, 'TRANS': 1205} Chain breaks: 4 Chain: "Aa" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.23, per 1000 atoms: 0.22 Number of scatterers: 10082 At special positions: 0 Unit cell: (78.514, 107.161, 144.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 3 15.00 O 1835 8.00 N 1664 7.00 C 6518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYSAa 712 " - pdb=" SG CYSAa 732 " distance=2.03 Simple disulfide: pdb=" SG CYSAa1402 " - pdb=" SG CYSAa1444 " distance=2.03 Simple disulfide: pdb=" SG CYSAa1418 " - pdb=" SG CYSAa1441 " distance=2.03 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: 0.74 Conformation dependent library (CDL) restraints added in 368.7 milliseconds 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2348 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 59.9% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'Aa' and resid 145 through 151 Processing helix chain 'Aa' and resid 192 through 201 Processing helix chain 'Aa' and resid 221 through 228 Processing helix chain 'Aa' and resid 229 through 231 No H-bonds generated for 'chain 'Aa' and resid 229 through 231' Processing helix chain 'Aa' and resid 247 through 258 Processing helix chain 'Aa' and resid 271 through 286 Processing helix chain 'Aa' and resid 287 through 291 removed outlier: 3.549A pdb=" N ARGAa 291 " --> pdb=" O SERAa 288 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 304 through 319 removed outlier: 3.634A pdb=" N LYSAa 309 " --> pdb=" O GLYAa 305 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARGAa 310 " --> pdb=" O GLYAa 306 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 334 through 352 removed outlier: 3.605A pdb=" N GLUAa 340 " --> pdb=" O ALAAa 336 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 364 through 369 Processing helix chain 'Aa' and resid 388 through 399 removed outlier: 4.415A pdb=" N LYSAa 392 " --> pdb=" O ALAAa 388 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLUAa 393 " --> pdb=" O THRAa 389 " (cutoff:3.500A) 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 449 Processing helix chain 'Aa' and resid 450 through 459 removed outlier: 3.697A pdb=" N GLUAa 454 " --> pdb=" O GLUAa 450 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYRAa 458 " --> pdb=" O GLUAa 454 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHEAa 459 " --> pdb=" O ILEAa 455 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 492 through 511 Processing helix chain 'Aa' and resid 512 through 531 removed outlier: 3.500A pdb=" N ILEAa 516 " --> pdb=" O PROAa 512 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 532 through 534 No H-bonds generated for 'chain 'Aa' and resid 532 through 534' 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 559 Processing helix chain 'Aa' and resid 561 through 563 No H-bonds generated for 'chain 'Aa' and resid 561 through 563' Processing helix chain 'Aa' and resid 564 through 581 removed outlier: 3.661A pdb=" N GLUAa 570 " --> pdb=" O METAa 566 " (cutoff:3.500A) Proline residue: Aa 573 - end of helix Processing helix chain 'Aa' and resid 585 through 614 Proline residue: Aa 599 - end of helix removed outlier: 3.847A pdb=" N VALAa 611 " --> pdb=" O SERAa 607 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHEAa 614 " --> pdb=" O PHEAa 610 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 621 through 650 Processing helix chain 'Aa' and resid 652 through 670 Proline residue: Aa 659 - end of helix Processing helix chain 'Aa' and resid 676 through 680 Processing helix chain 'Aa' and resid 681 through 690 removed outlier: 3.533A pdb=" N ARGAa 685 " --> pdb=" O LEUAa 681 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TRPAa 686 " --> pdb=" O GLYAa 682 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILEAa 690 " --> pdb=" O TRPAa 686 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 691 through 705 removed outlier: 4.244A pdb=" N TYRAa 695 " --> pdb=" O ASNAa 691 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VALAa 696 " --> pdb=" O PROAa 692 " (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 760 through 785 Processing helix chain 'Aa' and resid 898 through 910 removed outlier: 3.543A pdb=" N THRAa 902 " --> pdb=" O GLYAa 898 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THRAa 903 " --> pdb=" O ALAAa 899 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEUAa 904 " --> pdb=" O GLYAa 900 " (cutoff:3.500A) 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 Processing helix chain 'Aa' and resid 1002 through 1017 removed outlier: 3.622A pdb=" N GLUAa1014 " --> pdb=" O THRAa1010 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALAAa1017 " --> pdb=" O VALAa1013 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1033 through 1049 removed outlier: 3.517A pdb=" N TRPAa1038 " --> pdb=" O SERAa1034 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1064 through 1069 removed outlier: 3.616A pdb=" N PHEAa1069 " --> pdb=" O METAa1066 " (cutoff:3.500A) 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 1100 removed outlier: 3.501A pdb=" N PHEAa1098 " --> pdb=" O METAa1094 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1111 through 1120 removed outlier: 3.572A pdb=" N LEUAa1117 " --> pdb=" O ALAAa1113 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1134 through 1139 Processing helix chain 'Aa' and resid 1139 through 1158 removed outlier: 3.548A pdb=" N GLNAa1143 " --> pdb=" O SERAa1139 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALAAa1144 " --> pdb=" O SERAa1140 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILEAa1149 " --> pdb=" O VALAa1145 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYSAa1158 " --> pdb=" O ALAAa1154 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1174 through 1192 Processing helix chain 'Aa' and resid 1196 through 1215 removed outlier: 3.704A pdb=" N PHEAa1215 " --> pdb=" O ASNAa1211 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1221 through 1236 removed outlier: 3.689A pdb=" N GLNAa1226 " --> pdb=" O METAa1222 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHEAa1236 " --> pdb=" O VALAa1232 " (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 1296 removed outlier: 3.561A pdb=" N GLUAa1280 " --> pdb=" O GLNAa1276 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILEAa1281 " --> pdb=" O ILEAa1277 " (cutoff:3.500A) Proline residue: Aa1282 - end of helix Processing helix chain 'Aa' and resid 1300 through 1304 Processing helix chain 'Aa' and resid 1312 through 1339 removed outlier: 3.502A pdb=" N ALAAa1330 " --> pdb=" O TYRAa1326 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHEAa1339 " --> pdb=" O LEUAa1335 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1342 through 1360 removed outlier: 3.566A pdb=" N ALAAa1347 " --> pdb=" O ALAAa1343 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHEAa1360 " --> pdb=" O METAa1356 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1371 through 1373 No H-bonds generated for 'chain 'Aa' and resid 1371 through 1373' Processing helix chain 'Aa' and resid 1374 through 1381 removed outlier: 3.576A pdb=" N ARGAa1379 " --> pdb=" O ILEAa1375 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1381 through 1395 removed outlier: 4.374A pdb=" N TYRAa1385 " --> pdb=" O ASNAa1381 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEUAa1386 " --> pdb=" O PROAa1382 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1417 through 1429 Proline residue: Aa1424 - end of helix Processing helix chain 'Aa' and resid 1448 through 1456 removed outlier: 4.206A pdb=" N PHEAa1452 " --> pdb=" O SERAa1448 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SERAa1455 " --> pdb=" O THRAa1451 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VALAa1456 " --> pdb=" O PHEAa1452 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 1462 through 1489 Processing sheet with id=AA1, first strand: chain 'Aa' and resid 168 through 177 removed outlier: 5.641A pdb=" N LYSAa 171 " --> pdb=" O ALAAa 130 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ALAAa 130 " --> pdb=" O LYSAa 171 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALAAa 175 " --> pdb=" O ARGAa 126 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARGAa 126 " --> pdb=" O ALAAa 175 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N METAa 177 " --> pdb=" O GLYAa 124 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLYAa 124 " --> pdb=" O METAa 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Aa' and resid 168 through 177 removed outlier: 5.641A pdb=" N LYSAa 171 " --> pdb=" O ALAAa 130 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ALAAa 130 " --> pdb=" O LYSAa 171 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALAAa 175 " --> pdb=" O ARGAa 126 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARGAa 126 " --> pdb=" O ALAAa 175 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N METAa 177 " --> pdb=" O GLYAa 124 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLYAa 124 " --> pdb=" O METAa 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Aa' and resid 233 through 236 removed outlier: 6.254A pdb=" N THRAa 183 " --> pdb=" O ILEAa 358 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHEAa 384 " --> pdb=" O VALAa 376 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TYRAa 378 " --> pdb=" O GLNAa 382 " (cutoff:3.500A) removed outlier: 5.408A 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 876 through 885 removed outlier: 5.618A pdb=" N LEUAa 864 " --> pdb=" O HISAa 880 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASPAa 882 " --> pdb=" O ARGAa 862 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ARGAa 862 " --> pdb=" O ASPAa 882 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRPAa 884 " --> pdb=" O PHEAa 860 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHEAa 860 " --> pdb=" O TRPAa 884 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Aa' and resid 891 through 894 removed outlier: 6.430A pdb=" N ALAAa 892 " --> pdb=" O LEUAa1073 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEUAa1075 " --> pdb=" O ALAAa 892 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N METAa 894 " --> pdb=" O LEUAa1075 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEUAa1072 " --> pdb=" O PHEAa1084 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHEAa1084 " --> pdb=" O LEUAa1072 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHEAa1074 " --> pdb=" O ALAAa1082 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Aa' and resid 937 through 940 Processing sheet with id=AA8, first strand: chain 'Aa' and resid 1408 through 1409 removed outlier: 3.629A pdb=" N ALAAa1442 " --> pdb=" O GLUAa1434 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1494 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: 1.47 Time building geometry restraints manager: 1.02 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: 2109 1.33 - 1.45: 2610 1.45 - 1.58: 5528 1.58 - 1.70: 1 1.70 - 1.82: 101 Bond restraints: 10349 Sorted by residual: bond pdb=" N3B ANPAa1601 " pdb=" PG ANPAa1601 " ideal model delta sigma weight residual 1.795 1.545 0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" O3A ANPAa1601 " pdb=" PB ANPAa1601 " ideal model delta sigma weight residual 1.700 1.540 0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" N3B ANPAa1601 " pdb=" PB ANPAa1601 " ideal model delta sigma weight residual 1.669 1.574 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O3A ANPAa1601 " pdb=" PA ANPAa1601 " ideal model delta sigma weight residual 1.613 1.533 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" O2G ANPAa1601 " pdb=" PG ANPAa1601 " ideal model delta sigma weight residual 1.530 1.468 0.062 2.00e-02 2.50e+03 9.57e+00 ... (remaining 10344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 13724 2.52 - 5.04: 293 5.04 - 7.55: 24 7.55 - 10.07: 3 10.07 - 12.59: 4 Bond angle restraints: 14048 Sorted by residual: angle pdb=" CA ASPAa 511 " pdb=" CB ASPAa 511 " pdb=" CG ASPAa 511 " ideal model delta sigma weight residual 112.60 117.86 -5.26 1.00e+00 1.00e+00 2.76e+01 angle pdb=" CA PHEAa 559 " pdb=" CB PHEAa 559 " pdb=" CG PHEAa 559 " ideal model delta sigma weight residual 113.80 119.05 -5.25 1.00e+00 1.00e+00 2.76e+01 angle pdb=" CA ASPAa1033 " pdb=" CB ASPAa1033 " pdb=" CG ASPAa1033 " ideal model delta sigma weight residual 112.60 116.94 -4.34 1.00e+00 1.00e+00 1.88e+01 angle pdb=" C LYSAa 509 " pdb=" N GLYAa 510 " pdb=" CA GLYAa 510 " ideal model delta sigma weight residual 120.00 124.75 -4.75 1.10e+00 8.26e-01 1.86e+01 angle pdb=" C THRAa 293 " pdb=" N ASNAa 294 " pdb=" CA ASNAa 294 " ideal model delta sigma weight residual 120.71 126.79 -6.08 1.42e+00 4.96e-01 1.83e+01 ... (remaining 14043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.77: 5182 18.77 - 37.53: 632 37.53 - 56.30: 215 56.30 - 75.07: 37 75.07 - 93.83: 17 Dihedral angle restraints: 6083 sinusoidal: 2412 harmonic: 3671 Sorted by residual: dihedral pdb=" C ILEAa 514 " pdb=" N ILEAa 514 " pdb=" CA ILEAa 514 " pdb=" CB ILEAa 514 " ideal model delta harmonic sigma weight residual -122.00 -132.27 10.27 0 2.50e+00 1.60e-01 1.69e+01 dihedral pdb=" CA ASPAa 988 " pdb=" CB ASPAa 988 " pdb=" CG ASPAa 988 " pdb=" OD1 ASPAa 988 " ideal model delta sinusoidal sigma weight residual -30.00 -89.28 59.28 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" C5' ANPAa1601 " pdb=" C3' ANPAa1601 " pdb=" C4' ANPAa1601 " pdb=" O3' ANPAa1601 " ideal model delta sinusoidal sigma weight residual -74.79 -168.62 93.83 1 3.00e+01 1.11e-03 1.14e+01 ... (remaining 6080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1424 0.091 - 0.182: 91 0.182 - 0.273: 8 0.273 - 0.364: 0 0.364 - 0.455: 1 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C3' ANPAa1601 " pdb=" C2' ANPAa1601 " pdb=" C4' ANPAa1601 " pdb=" O3' ANPAa1601 " both_signs ideal model delta sigma weight residual False -2.36 -2.81 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA ILEAa 514 " pdb=" N ILEAa 514 " pdb=" C ILEAa 514 " pdb=" CB ILEAa 514 " both_signs ideal model delta sigma weight residual False 2.43 2.18 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ASPAa 511 " pdb=" N ASPAa 511 " pdb=" C ASPAa 511 " pdb=" CB ASPAa 511 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1521 not shown) Planarity restraints: 1781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYRAa 361 " 0.111 2.00e-02 2.50e+03 5.68e-02 6.45e+01 pdb=" CG TYRAa 361 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYRAa 361 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TYRAa 361 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYRAa 361 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYRAa 361 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYRAa 361 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYRAa 361 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANPAa1601 " -0.063 2.00e-02 2.50e+03 3.27e-02 2.94e+01 pdb=" C2 ANPAa1601 " 0.005 2.00e-02 2.50e+03 pdb=" C4 ANPAa1601 " 0.036 2.00e-02 2.50e+03 pdb=" C5 ANPAa1601 " 0.036 2.00e-02 2.50e+03 pdb=" C6 ANPAa1601 " 0.013 2.00e-02 2.50e+03 pdb=" C8 ANPAa1601 " -0.001 2.00e-02 2.50e+03 pdb=" N1 ANPAa1601 " 0.003 2.00e-02 2.50e+03 pdb=" N3 ANPAa1601 " -0.006 2.00e-02 2.50e+03 pdb=" N6 ANPAa1601 " -0.064 2.00e-02 2.50e+03 pdb=" N7 ANPAa1601 " 0.015 2.00e-02 2.50e+03 pdb=" N9 ANPAa1601 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRPAa 326 " 0.051 2.00e-02 2.50e+03 2.72e-02 1.85e+01 pdb=" CG TRPAa 326 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRPAa 326 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRPAa 326 " -0.027 2.00e-02 2.50e+03 pdb=" NE1 TRPAa 326 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRPAa 326 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRPAa 326 " -0.042 2.00e-02 2.50e+03 pdb=" CZ2 TRPAa 326 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRPAa 326 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRPAa 326 " 0.038 2.00e-02 2.50e+03 ... (remaining 1778 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 133 2.63 - 3.20: 9008 3.20 - 3.77: 16260 3.77 - 4.33: 22154 4.33 - 4.90: 36694 Nonbonded interactions: 84249 Sorted by model distance: nonbonded pdb=" O LEUAa 929 " pdb=" OD1 ASPAa 930 " model vdw 2.063 3.040 nonbonded pdb=" OG SERAa 587 " pdb=" OE1 GLUAa 784 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASPAa 334 " pdb=" OG1 THRAa 337 " model vdw 2.215 3.040 nonbonded pdb=" O VALAa 143 " pdb=" OH TYRAa1198 " model vdw 2.221 3.040 nonbonded pdb=" O PHEAa1210 " pdb=" OG SERAa1214 " model vdw 2.233 3.040 ... (remaining 84244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 9.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:8.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 0.250 10352 Z= 0.300 Angle : 0.784 12.588 14054 Z= 0.451 Chirality : 0.048 0.455 1524 Planarity : 0.005 0.057 1781 Dihedral : 18.819 93.833 3726 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 6.90 % Allowed : 26.19 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.24), residues: 1249 helix: 0.86 (0.19), residues: 676 sheet: -1.59 (0.50), residues: 94 loop : -0.22 (0.31), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAa 188 TYR 0.111 0.002 TYRAa 361 PHE 0.046 0.003 PHEAa 371 TRP 0.051 0.002 TRPAa 326 HIS 0.005 0.001 HISAa 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.30 (10349) covalent geometry : angle 0.78460 / 0.45 (14048) SS BOND : bond 0.00337 / 0.16 ( 3) SS BOND : angle 0.32477 / 0.14 ( 6) hydrogen bonds : bond 0.22615 / 14.71 ( 514) hydrogen bonds : angle 7.01175 / 4.96 ( 1494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 149 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: Aa 511 ASP cc_start: 0.8170 (p0) cc_final: 0.7932 (p0) REVERT: Aa 894 MET cc_start: 0.8530 (mtp) cc_final: 0.8124 (mtt) outliers start: 74 outliers final: 63 residues processed: 219 average time/residue: 0.3709 time to fit residues: 90.0916 Evaluate side-chains 204 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 141 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 123 ILE Chi-restraints excluded: chain Aa residue 174 ASP Chi-restraints excluded: chain Aa residue 204 THR Chi-restraints excluded: chain Aa residue 216 THR Chi-restraints excluded: chain Aa residue 264 ARG Chi-restraints excluded: chain Aa residue 272 THR Chi-restraints excluded: chain Aa residue 288 SER Chi-restraints excluded: chain Aa residue 290 THR Chi-restraints excluded: chain Aa residue 298 ASP Chi-restraints excluded: chain Aa residue 312 SER Chi-restraints excluded: chain Aa residue 319 SER Chi-restraints excluded: chain Aa residue 348 SER Chi-restraints excluded: chain Aa residue 396 GLU Chi-restraints excluded: chain Aa residue 408 THR Chi-restraints excluded: chain Aa residue 444 ASN Chi-restraints excluded: chain Aa residue 448 TYR Chi-restraints excluded: chain Aa residue 492 SER Chi-restraints excluded: chain Aa residue 530 SER Chi-restraints excluded: chain Aa residue 539 THR Chi-restraints excluded: chain Aa residue 565 ILE Chi-restraints excluded: chain Aa residue 566 MET Chi-restraints excluded: chain Aa residue 587 SER Chi-restraints excluded: chain Aa residue 645 SER Chi-restraints excluded: chain Aa residue 649 VAL Chi-restraints excluded: chain Aa residue 652 SER Chi-restraints excluded: chain Aa residue 696 VAL Chi-restraints excluded: chain Aa residue 699 SER Chi-restraints excluded: chain Aa residue 716 VAL Chi-restraints excluded: chain Aa residue 778 ILE Chi-restraints excluded: chain Aa residue 856 ARG Chi-restraints excluded: chain Aa residue 874 ASP Chi-restraints excluded: chain Aa residue 876 VAL Chi-restraints excluded: chain Aa residue 901 LYS Chi-restraints excluded: chain Aa residue 902 THR Chi-restraints excluded: chain Aa residue 905 LEU Chi-restraints excluded: chain Aa residue 907 CYS Chi-restraints excluded: chain Aa residue 912 VAL Chi-restraints excluded: chain Aa residue 913 THR Chi-restraints excluded: chain Aa residue 914 THR Chi-restraints excluded: chain Aa residue 929 LEU Chi-restraints excluded: chain Aa residue 959 SER Chi-restraints excluded: chain Aa residue 965 SER Chi-restraints excluded: chain Aa residue 966 ASN Chi-restraints excluded: chain Aa residue 980 VAL Chi-restraints excluded: chain Aa residue 1016 VAL Chi-restraints excluded: chain Aa residue 1057 THR Chi-restraints excluded: chain Aa residue 1139 SER Chi-restraints excluded: chain Aa residue 1140 SER Chi-restraints excluded: chain Aa residue 1157 SER Chi-restraints excluded: chain Aa residue 1177 LYS Chi-restraints excluded: chain Aa residue 1268 SER Chi-restraints excluded: chain Aa residue 1273 ILE Chi-restraints excluded: chain Aa residue 1287 VAL Chi-restraints excluded: chain Aa residue 1308 THR Chi-restraints excluded: chain Aa residue 1314 ARG Chi-restraints excluded: chain Aa residue 1344 ASP Chi-restraints excluded: chain Aa residue 1349 LEU Chi-restraints excluded: chain Aa residue 1358 LEU Chi-restraints excluded: chain Aa residue 1393 THR Chi-restraints excluded: chain Aa residue 1408 VAL Chi-restraints excluded: chain Aa residue 1409 SER Chi-restraints excluded: chain Aa residue 1440 SER Chi-restraints excluded: chain Aa residue 1454 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [108, 49, 97, 113, 53, 5, 33, 123, 65, 62, 51] chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 417 ASN Aa 867 GLN Aa 880 HIS Aa1035 GLN ** Aa1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1111 ASN Aa1138 ASN Aa1143 GLN Aa1178 GLN Aa1245 GLN Aa1284 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115440 restraints weight = 14844.984| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.33 r_work: 0.3332 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10352 Z= 0.136 Angle : 0.554 7.021 14054 Z= 0.284 Chirality : 0.041 0.212 1524 Planarity : 0.004 0.038 1781 Dihedral : 9.976 59.830 1517 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 6.24 % Allowed : 25.07 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.24), residues: 1249 helix: 1.38 (0.19), residues: 683 sheet: -1.50 (0.51), residues: 90 loop : -0.26 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAa 126 TYR 0.016 0.001 TYRAa 361 PHE 0.018 0.002 PHEAa1376 TRP 0.012 0.001 TRPAa 442 HIS 0.002 0.001 HISAa 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (10349) covalent geometry : angle 0.55438 / 0.28 (14048) SS BOND : bond 0.00453 / 0.22 ( 3) SS BOND : angle 0.47683 / 0.19 ( 6) hydrogen bonds : bond 0.04533 / 2.88 ( 514) hydrogen bonds : angle 4.60603 / 3.27 ( 1494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 168 time to evaluate : 0.402 Fit side-chains REVERT: Aa 250 ASP cc_start: 0.8484 (m-30) cc_final: 0.8213 (m-30) REVERT: Aa 372 ASP cc_start: 0.8465 (m-30) cc_final: 0.7495 (t0) REVERT: Aa 544 TYR cc_start: 0.8534 (t80) cc_final: 0.8244 (t80) REVERT: Aa 894 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8074 (mtt) REVERT: Aa 912 VAL cc_start: 0.7215 (OUTLIER) cc_final: 0.6916 (t) REVERT: Aa 943 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: Aa 1068 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7220 (mm-30) REVERT: Aa 1095 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8555 (mp) REVERT: Aa 1409 SER cc_start: 0.8809 (m) cc_final: 0.8259 (p) REVERT: Aa 1481 THR cc_start: 0.8897 (m) cc_final: 0.8640 (p) outliers start: 67 outliers final: 29 residues processed: 218 average time/residue: 0.4108 time to fit residues: 98.6175 Evaluate side-chains 180 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 202 VAL Chi-restraints excluded: chain Aa residue 204 THR Chi-restraints excluded: chain Aa residue 264 ARG Chi-restraints excluded: chain Aa residue 312 SER Chi-restraints excluded: chain Aa residue 348 SER Chi-restraints excluded: chain Aa residue 396 GLU Chi-restraints excluded: chain Aa residue 424 LEU Chi-restraints excluded: chain Aa residue 434 THR Chi-restraints excluded: chain Aa residue 448 TYR Chi-restraints excluded: chain Aa residue 508 MET Chi-restraints excluded: chain Aa residue 529 LEU Chi-restraints excluded: chain Aa residue 530 SER Chi-restraints excluded: chain Aa residue 649 VAL Chi-restraints excluded: chain Aa residue 696 VAL Chi-restraints excluded: chain Aa residue 876 VAL Chi-restraints excluded: chain Aa residue 894 MET Chi-restraints excluded: chain Aa residue 902 THR Chi-restraints excluded: chain Aa residue 912 VAL Chi-restraints excluded: chain Aa residue 913 THR Chi-restraints excluded: chain Aa residue 914 THR Chi-restraints excluded: chain Aa residue 943 GLN Chi-restraints excluded: chain Aa residue 980 VAL Chi-restraints excluded: chain Aa residue 1016 VAL Chi-restraints excluded: chain Aa residue 1057 THR Chi-restraints excluded: chain Aa residue 1066 MET Chi-restraints excluded: chain Aa residue 1068 GLU Chi-restraints excluded: chain Aa residue 1095 ILE Chi-restraints excluded: chain Aa residue 1140 SER Chi-restraints excluded: chain Aa residue 1308 THR Chi-restraints excluded: chain Aa residue 1349 LEU Chi-restraints excluded: chain Aa residue 1363 VAL Chi-restraints excluded: chain Aa residue 1395 LEU Chi-restraints excluded: chain Aa residue 1408 VAL Chi-restraints excluded: chain Aa residue 1476 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [0, 55, 69, 43, 54, 95, 50, 87, 49, 59, 86] chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 0.0070 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 95 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 417 ASN Aa 522 GLN Aa1035 GLN ** Aa1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1178 GLN Aa1223 GLN ** Aa1359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117245 restraints weight = 14768.021| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.36 r_work: 0.3349 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10352 Z= 0.114 Angle : 0.510 7.269 14054 Z= 0.261 Chirality : 0.040 0.221 1524 Planarity : 0.004 0.037 1781 Dihedral : 7.314 58.700 1445 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.78 % Allowed : 25.07 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.24), residues: 1249 helix: 1.60 (0.19), residues: 690 sheet: -1.45 (0.51), residues: 87 loop : -0.31 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAa 126 TYR 0.015 0.001 TYRAa 989 PHE 0.016 0.001 PHEAa 552 TRP 0.011 0.001 TRPAa 442 HIS 0.002 0.000 HISAa 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (10349) covalent geometry : angle 0.51037 / 0.26 (14048) SS BOND : bond 0.00253 / 0.12 ( 3) SS BOND : angle 0.29437 / 0.13 ( 6) hydrogen bonds : bond 0.03874 / 2.48 ( 514) hydrogen bonds : angle 4.25066 / 3.02 ( 1494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 167 time to evaluate : 0.312 Fit side-chains REVERT: Aa 372 ASP cc_start: 0.8490 (m-30) cc_final: 0.7584 (t0) REVERT: Aa 396 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: Aa 544 TYR cc_start: 0.8514 (t80) cc_final: 0.8313 (t80) REVERT: Aa 894 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8140 (mtt) REVERT: Aa 943 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: Aa 1004 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: Aa 1068 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7194 (mm-30) REVERT: Aa 1178 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8183 (mt0) REVERT: Aa 1409 SER cc_start: 0.8751 (m) cc_final: 0.8300 (p) REVERT: Aa 1476 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7684 (mp) outliers start: 62 outliers final: 21 residues processed: 209 average time/residue: 0.4132 time to fit residues: 95.0598 Evaluate side-chains 178 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 202 VAL Chi-restraints excluded: chain Aa residue 264 ARG Chi-restraints excluded: chain Aa residue 298 ASP Chi-restraints excluded: chain Aa residue 348 SER Chi-restraints excluded: chain Aa residue 396 GLU Chi-restraints excluded: chain Aa residue 424 LEU Chi-restraints excluded: chain Aa residue 434 THR Chi-restraints excluded: chain Aa residue 448 TYR Chi-restraints excluded: chain Aa residue 649 VAL Chi-restraints excluded: chain Aa residue 657 MET Chi-restraints excluded: chain Aa residue 716 VAL Chi-restraints excluded: chain Aa residue 778 ILE Chi-restraints excluded: chain Aa residue 876 VAL Chi-restraints excluded: chain Aa residue 894 MET Chi-restraints excluded: chain Aa residue 905 LEU Chi-restraints excluded: chain Aa residue 914 THR Chi-restraints excluded: chain Aa residue 943 GLN Chi-restraints excluded: chain Aa residue 1004 GLU Chi-restraints excluded: chain Aa residue 1066 MET Chi-restraints excluded: chain Aa residue 1068 GLU Chi-restraints excluded: chain Aa residue 1178 GLN Chi-restraints excluded: chain Aa residue 1308 THR Chi-restraints excluded: chain Aa residue 1344 ASP Chi-restraints excluded: chain Aa residue 1349 LEU Chi-restraints excluded: chain Aa residue 1395 LEU Chi-restraints excluded: chain Aa residue 1408 VAL Chi-restraints excluded: chain Aa residue 1457 ASN Chi-restraints excluded: chain Aa residue 1476 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [89, 76, 113, 14, 11, 53, 47, 13, 111, 45, 61] chunk 89 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 113 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 522 GLN Aa1035 GLN ** Aa1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.135214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115565 restraints weight = 14793.777| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.33 r_work: 0.3325 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10352 Z= 0.150 Angle : 0.536 9.980 14054 Z= 0.274 Chirality : 0.041 0.196 1524 Planarity : 0.004 0.037 1781 Dihedral : 6.761 59.656 1434 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.13 % Allowed : 26.37 % Favored : 68.50 % 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: 0.91 (0.24), residues: 1249 helix: 1.62 (0.19), residues: 685 sheet: -1.58 (0.49), residues: 87 loop : -0.39 (0.31), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAa1405 TYR 0.017 0.001 TYRAa 989 PHE 0.015 0.001 PHEAa 552 TRP 0.009 0.001 TRPAa 442 HIS 0.002 0.000 HISAa 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (10349) covalent geometry : angle 0.53613 / 0.27 (14048) SS BOND : bond 0.00379 / 0.19 ( 3) SS BOND : angle 0.31017 / 0.14 ( 6) hydrogen bonds : bond 0.03894 / 2.51 ( 514) hydrogen bonds : angle 4.19447 / 2.98 ( 1494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 0.382 Fit side-chains REVERT: Aa 227 ARG cc_start: 0.7560 (ttp80) cc_final: 0.7119 (ttm110) REVERT: Aa 372 ASP cc_start: 0.8542 (m-30) cc_final: 0.7773 (t70) REVERT: Aa 396 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: Aa 610 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7632 (t80) REVERT: Aa 765 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8393 (tt) REVERT: Aa 894 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8059 (mtt) REVERT: Aa 943 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: Aa 1004 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: Aa 1068 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7194 (mm-30) REVERT: Aa 1148 GLU cc_start: 0.7595 (tp30) cc_final: 0.7066 (tp30) REVERT: Aa 1152 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7621 (ttm) REVERT: Aa 1409 SER cc_start: 0.8768 (m) cc_final: 0.8338 (p) REVERT: Aa 1476 ILE cc_start: 0.8041 (mt) cc_final: 0.7730 (mp) REVERT: Aa 1480 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8708 (mt) outliers start: 55 outliers final: 28 residues processed: 198 average time/residue: 0.4181 time to fit residues: 91.2959 Evaluate side-chains 185 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 123 ILE Chi-restraints excluded: chain Aa residue 202 VAL Chi-restraints excluded: chain Aa residue 264 ARG Chi-restraints excluded: chain Aa residue 348 SER Chi-restraints excluded: chain Aa residue 396 GLU Chi-restraints excluded: chain Aa residue 424 LEU Chi-restraints excluded: chain Aa residue 434 THR Chi-restraints excluded: chain Aa residue 448 TYR Chi-restraints excluded: chain Aa residue 516 ILE Chi-restraints excluded: chain Aa residue 610 PHE Chi-restraints excluded: chain Aa residue 645 SER Chi-restraints excluded: chain Aa residue 649 VAL Chi-restraints excluded: chain Aa residue 657 MET Chi-restraints excluded: chain Aa residue 696 VAL Chi-restraints excluded: chain Aa residue 716 VAL Chi-restraints excluded: chain Aa residue 765 LEU Chi-restraints excluded: chain Aa residue 778 ILE Chi-restraints excluded: chain Aa residue 876 VAL Chi-restraints excluded: chain Aa residue 894 MET Chi-restraints excluded: chain Aa residue 905 LEU Chi-restraints excluded: chain Aa residue 914 THR Chi-restraints excluded: chain Aa residue 929 LEU Chi-restraints excluded: chain Aa residue 943 GLN Chi-restraints excluded: chain Aa residue 1004 GLU Chi-restraints excluded: chain Aa residue 1016 VAL Chi-restraints excluded: chain Aa residue 1066 MET Chi-restraints excluded: chain Aa residue 1068 GLU Chi-restraints excluded: chain Aa residue 1152 MET Chi-restraints excluded: chain Aa residue 1181 LEU Chi-restraints excluded: chain Aa residue 1308 THR Chi-restraints excluded: chain Aa residue 1344 ASP Chi-restraints excluded: chain Aa residue 1349 LEU Chi-restraints excluded: chain Aa residue 1395 LEU Chi-restraints excluded: chain Aa residue 1400 VAL Chi-restraints excluded: chain Aa residue 1408 VAL Chi-restraints excluded: chain Aa residue 1457 ASN Chi-restraints excluded: chain Aa residue 1480 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [92, 98, 73, 17, 61, 81, 115, 85, 15, 51, 49] chunk 92 optimal weight: 0.0170 chunk 98 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 417 ASN Aa 522 GLN Aa1035 GLN ** Aa1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa1178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.116393 restraints weight = 14739.515| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.31 r_work: 0.3323 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10352 Z= 0.143 Angle : 0.533 9.689 14054 Z= 0.273 Chirality : 0.041 0.203 1524 Planarity : 0.004 0.037 1781 Dihedral : 6.594 58.150 1434 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.50 % Allowed : 26.93 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.24), residues: 1249 helix: 1.65 (0.19), residues: 685 sheet: -1.65 (0.49), residues: 87 loop : -0.39 (0.31), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAa1405 TYR 0.019 0.001 TYRAa 989 PHE 0.030 0.002 PHEAa1376 TRP 0.010 0.001 TRPAa 442 HIS 0.002 0.000 HISAa 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (10349) covalent geometry : angle 0.53349 / 0.27 (14048) SS BOND : bond 0.00347 / 0.17 ( 3) SS BOND : angle 0.30218 / 0.14 ( 6) hydrogen bonds : bond 0.03736 / 2.39 ( 514) hydrogen bonds : angle 4.13074 / 2.93 ( 1494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 163 time to evaluate : 0.390 Fit side-chains REVERT: Aa 181 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7551 (mt-10) REVERT: Aa 227 ARG cc_start: 0.7557 (ttp80) cc_final: 0.7137 (ttm110) REVERT: Aa 372 ASP cc_start: 0.8529 (m-30) cc_final: 0.7816 (t70) REVERT: Aa 610 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7701 (t80) REVERT: Aa 765 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8425 (tt) REVERT: Aa 943 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7315 (mp10) REVERT: Aa 1004 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7879 (tp30) REVERT: Aa 1066 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7877 (mmt) REVERT: Aa 1068 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7166 (mm-30) REVERT: Aa 1148 GLU cc_start: 0.7690 (tp30) cc_final: 0.7424 (tp30) REVERT: Aa 1409 SER cc_start: 0.8783 (m) cc_final: 0.8345 (p) REVERT: Aa 1476 ILE cc_start: 0.8110 (mt) cc_final: 0.7821 (mp) REVERT: Aa 1480 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8691 (mt) outliers start: 59 outliers final: 29 residues processed: 202 average time/residue: 0.4025 time to fit residues: 89.4422 Evaluate side-chains 184 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 123 ILE Chi-restraints excluded: chain Aa residue 202 VAL Chi-restraints excluded: chain Aa residue 264 ARG Chi-restraints excluded: chain Aa residue 298 ASP Chi-restraints excluded: chain Aa residue 424 LEU Chi-restraints excluded: chain Aa residue 434 THR Chi-restraints excluded: chain Aa residue 448 TYR Chi-restraints excluded: chain Aa residue 516 ILE Chi-restraints excluded: chain Aa residue 539 THR Chi-restraints excluded: chain Aa residue 610 PHE Chi-restraints excluded: chain Aa residue 645 SER Chi-restraints excluded: chain Aa residue 649 VAL Chi-restraints excluded: chain Aa residue 657 MET Chi-restraints excluded: chain Aa residue 716 VAL Chi-restraints excluded: chain Aa residue 765 LEU Chi-restraints excluded: chain Aa residue 778 ILE Chi-restraints excluded: chain Aa residue 876 VAL Chi-restraints excluded: chain Aa residue 905 LEU Chi-restraints excluded: chain Aa residue 912 VAL Chi-restraints excluded: chain Aa residue 914 THR Chi-restraints excluded: chain Aa residue 929 LEU Chi-restraints excluded: chain Aa residue 943 GLN Chi-restraints excluded: chain Aa residue 944 ASP Chi-restraints excluded: chain Aa residue 1004 GLU Chi-restraints excluded: chain Aa residue 1016 VAL Chi-restraints excluded: chain Aa residue 1066 MET Chi-restraints excluded: chain Aa residue 1068 GLU Chi-restraints excluded: chain Aa residue 1181 LEU Chi-restraints excluded: chain Aa residue 1344 ASP Chi-restraints excluded: chain Aa residue 1349 LEU Chi-restraints excluded: chain Aa residue 1363 VAL Chi-restraints excluded: chain Aa residue 1395 LEU Chi-restraints excluded: chain Aa residue 1400 VAL Chi-restraints excluded: chain Aa residue 1408 VAL Chi-restraints excluded: chain Aa residue 1457 ASN Chi-restraints excluded: chain Aa residue 1480 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [28, 81, 33, 21, 117, 67, 43, 39, 61, 80, 55] chunk 28 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 67 optimal weight: 0.0970 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 55 optimal weight: 0.0980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 417 ASN Aa 522 GLN Aa1035 GLN Aa1076 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.136726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117089 restraints weight = 14916.385| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.35 r_work: 0.3347 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10352 Z= 0.112 Angle : 0.517 8.641 14054 Z= 0.265 Chirality : 0.040 0.210 1524 Planarity : 0.004 0.036 1781 Dihedral : 6.005 55.237 1429 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.66 % Allowed : 27.68 % Favored : 67.66 % 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: 1.01 (0.24), residues: 1249 helix: 1.70 (0.19), residues: 689 sheet: -1.53 (0.48), residues: 97 loop : -0.32 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAa 126 TYR 0.018 0.001 TYRAa 989 PHE 0.017 0.001 PHEAa 552 TRP 0.010 0.001 TRPAa 442 HIS 0.002 0.000 HISAa 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (10349) covalent geometry : angle 0.51704 / 0.26 (14048) SS BOND : bond 0.00227 / 0.11 ( 3) SS BOND : angle 0.28016 / 0.12 ( 6) hydrogen bonds : bond 0.03422 / 2.18 ( 514) hydrogen bonds : angle 4.06204 / 2.88 ( 1494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 0.400 Fit side-chains REVERT: Aa 227 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7122 (ttm110) REVERT: Aa 508 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6842 (mtt) REVERT: Aa 610 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7717 (t80) REVERT: Aa 657 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7315 (ttp) REVERT: Aa 765 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8389 (tt) REVERT: Aa 943 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7235 (mp10) REVERT: Aa 1004 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7850 (tp30) REVERT: Aa 1066 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7726 (mmt) REVERT: Aa 1068 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7178 (mm-30) REVERT: Aa 1409 SER cc_start: 0.8741 (m) cc_final: 0.8353 (p) REVERT: Aa 1476 ILE cc_start: 0.8086 (mt) cc_final: 0.7785 (mp) REVERT: Aa 1480 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8706 (mt) outliers start: 50 outliers final: 21 residues processed: 196 average time/residue: 0.3834 time to fit residues: 83.5346 Evaluate side-chains 177 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 202 VAL Chi-restraints excluded: chain Aa residue 264 ARG Chi-restraints excluded: chain Aa residue 348 SER Chi-restraints excluded: chain Aa residue 424 LEU Chi-restraints excluded: chain Aa residue 434 THR Chi-restraints excluded: chain Aa residue 448 TYR Chi-restraints excluded: chain Aa residue 508 MET Chi-restraints excluded: chain Aa residue 610 PHE Chi-restraints excluded: chain Aa residue 649 VAL Chi-restraints excluded: chain Aa residue 657 MET Chi-restraints excluded: chain Aa residue 696 VAL Chi-restraints excluded: chain Aa residue 716 VAL Chi-restraints excluded: chain Aa residue 732 CYS Chi-restraints excluded: chain Aa residue 765 LEU Chi-restraints excluded: chain Aa residue 778 ILE Chi-restraints excluded: chain Aa residue 876 VAL Chi-restraints excluded: chain Aa residue 905 LEU Chi-restraints excluded: chain Aa residue 914 THR Chi-restraints excluded: chain Aa residue 929 LEU Chi-restraints excluded: chain Aa residue 943 GLN Chi-restraints excluded: chain Aa residue 951 THR Chi-restraints excluded: chain Aa residue 1004 GLU Chi-restraints excluded: chain Aa residue 1016 VAL Chi-restraints excluded: chain Aa residue 1066 MET Chi-restraints excluded: chain Aa residue 1068 GLU Chi-restraints excluded: chain Aa residue 1168 LEU Chi-restraints excluded: chain Aa residue 1395 LEU Chi-restraints excluded: chain Aa residue 1400 VAL Chi-restraints excluded: chain Aa residue 1408 VAL Chi-restraints excluded: chain Aa residue 1480 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [29, 122, 30, 85, 34, 32, 31, 84, 43, 92, 120] chunk 29 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 85 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 0.0050 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 417 ASN Aa 522 GLN Aa1035 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.136172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.117132 restraints weight = 14709.751| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.22 r_work: 0.3340 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10352 Z= 0.142 Angle : 0.548 9.491 14054 Z= 0.280 Chirality : 0.041 0.208 1524 Planarity : 0.004 0.036 1781 Dihedral : 5.906 54.198 1427 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.03 % Allowed : 27.68 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.24), residues: 1249 helix: 1.67 (0.19), residues: 689 sheet: -1.59 (0.46), residues: 100 loop : -0.36 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAa1405 TYR 0.021 0.001 TYRAa 989 PHE 0.037 0.002 PHEAa1376 TRP 0.010 0.001 TRPAa 442 HIS 0.002 0.000 HISAa 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (10349) covalent geometry : angle 0.54826 / 0.28 (14048) SS BOND : bond 0.00346 / 0.17 ( 3) SS BOND : angle 0.31430 / 0.14 ( 6) hydrogen bonds : bond 0.03584 / 2.29 ( 514) hydrogen bonds : angle 4.08695 / 2.90 ( 1494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 156 time to evaluate : 0.373 Fit side-chains REVERT: Aa 264 ARG cc_start: 0.6351 (OUTLIER) cc_final: 0.4636 (ppt170) REVERT: Aa 508 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6942 (mtt) REVERT: Aa 585 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8144 (mtt-85) REVERT: Aa 610 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7743 (t80) REVERT: Aa 657 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7394 (ttp) REVERT: Aa 765 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8446 (tt) REVERT: Aa 943 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7273 (mp10) REVERT: Aa 1004 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7896 (tp30) REVERT: Aa 1066 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7910 (mmt) REVERT: Aa 1068 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7169 (mm-30) REVERT: Aa 1409 SER cc_start: 0.8763 (m) cc_final: 0.8341 (p) REVERT: Aa 1476 ILE cc_start: 0.8197 (mt) cc_final: 0.7907 (mp) REVERT: Aa 1480 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8746 (mt) outliers start: 54 outliers final: 25 residues processed: 195 average time/residue: 0.3871 time to fit residues: 83.5727 Evaluate side-chains 186 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 123 ILE Chi-restraints excluded: chain Aa residue 202 VAL Chi-restraints excluded: chain Aa residue 264 ARG Chi-restraints excluded: chain Aa residue 348 SER Chi-restraints excluded: chain Aa residue 424 LEU Chi-restraints excluded: chain Aa residue 434 THR Chi-restraints excluded: chain Aa residue 508 MET Chi-restraints excluded: chain Aa residue 585 ARG Chi-restraints excluded: chain Aa residue 591 LEU Chi-restraints excluded: chain Aa residue 610 PHE Chi-restraints excluded: chain Aa residue 645 SER Chi-restraints excluded: chain Aa residue 649 VAL Chi-restraints excluded: chain Aa residue 657 MET Chi-restraints excluded: chain Aa residue 696 VAL Chi-restraints excluded: chain Aa residue 716 VAL Chi-restraints excluded: chain Aa residue 765 LEU Chi-restraints excluded: chain Aa residue 778 ILE Chi-restraints excluded: chain Aa residue 876 VAL Chi-restraints excluded: chain Aa residue 894 MET Chi-restraints excluded: chain Aa residue 905 LEU Chi-restraints excluded: chain Aa residue 912 VAL Chi-restraints excluded: chain Aa residue 914 THR Chi-restraints excluded: chain Aa residue 929 LEU Chi-restraints excluded: chain Aa residue 943 GLN Chi-restraints excluded: chain Aa residue 944 ASP Chi-restraints excluded: chain Aa residue 951 THR Chi-restraints excluded: chain Aa residue 1004 GLU Chi-restraints excluded: chain Aa residue 1016 VAL Chi-restraints excluded: chain Aa residue 1066 MET Chi-restraints excluded: chain Aa residue 1068 GLU Chi-restraints excluded: chain Aa residue 1168 LEU Chi-restraints excluded: chain Aa residue 1363 VAL Chi-restraints excluded: chain Aa residue 1395 LEU Chi-restraints excluded: chain Aa residue 1400 VAL Chi-restraints excluded: chain Aa residue 1408 VAL Chi-restraints excluded: chain Aa residue 1480 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [2, 98, 48, 50, 93, 27, 24, 81, 37, 97, 8] chunk 2 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Aa 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 522 GLN ** Aa 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa1035 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 = 0.3677 r_free = 0.3677 target = 0.135957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.116398 restraints weight = 14752.727| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.32 r_work: 0.3314 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10352 Z= 0.148 Angle : 0.560 9.071 14054 Z= 0.285 Chirality : 0.042 0.199 1524 Planarity : 0.004 0.036 1781 Dihedral : 5.806 54.304 1425 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.66 % Allowed : 27.96 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.24), residues: 1249 helix: 1.64 (0.19), residues: 689 sheet: -1.68 (0.46), residues: 100 loop : -0.39 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAa1405 TYR 0.026 0.001 TYRAa 448 PHE 0.025 0.001 PHEAa 552 TRP 0.010 0.001 TRPAa 442 HIS 0.001 0.000 HISAa 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (10349) covalent geometry : angle 0.55998 / 0.28 (14048) SS BOND : bond 0.00350 / 0.17 ( 3) SS BOND : angle 0.30021 / 0.14 ( 6) hydrogen bonds : bond 0.03598 / 2.29 ( 514) hydrogen bonds : angle 4.08682 / 2.90 ( 1494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 264 ARG cc_start: 0.6423 (OUTLIER) cc_final: 0.4725 (ppt170) REVERT: Aa 508 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6875 (mtt) REVERT: Aa 610 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7749 (t80) REVERT: Aa 657 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7329 (ttp) REVERT: Aa 765 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8403 (tt) REVERT: Aa 943 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7229 (mp10) REVERT: Aa 1004 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7870 (tp30) REVERT: Aa 1066 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7850 (mmt) REVERT: Aa 1409 SER cc_start: 0.8772 (m) cc_final: 0.8368 (p) REVERT: Aa 1476 ILE cc_start: 0.8131 (mt) cc_final: 0.7853 (mp) REVERT: Aa 1480 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8704 (mt) outliers start: 50 outliers final: 31 residues processed: 192 average time/residue: 0.3800 time to fit residues: 81.1889 Evaluate side-chains 190 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 123 ILE Chi-restraints excluded: chain Aa residue 202 VAL Chi-restraints excluded: chain Aa residue 264 ARG Chi-restraints excluded: chain Aa residue 298 ASP Chi-restraints excluded: chain Aa residue 348 SER Chi-restraints excluded: chain Aa residue 383 ILE Chi-restraints excluded: chain Aa residue 434 THR Chi-restraints excluded: chain Aa residue 508 MET Chi-restraints excluded: chain Aa residue 516 ILE Chi-restraints excluded: chain Aa residue 539 THR Chi-restraints excluded: chain Aa residue 591 LEU Chi-restraints excluded: chain Aa residue 610 PHE Chi-restraints excluded: chain Aa residue 645 SER Chi-restraints excluded: chain Aa residue 649 VAL Chi-restraints excluded: chain Aa residue 657 MET Chi-restraints excluded: chain Aa residue 696 VAL Chi-restraints excluded: chain Aa residue 705 PHE Chi-restraints excluded: chain Aa residue 716 VAL Chi-restraints excluded: chain Aa residue 765 LEU Chi-restraints excluded: chain Aa residue 778 ILE Chi-restraints excluded: chain Aa residue 876 VAL Chi-restraints excluded: chain Aa residue 894 MET Chi-restraints excluded: chain Aa residue 905 LEU Chi-restraints excluded: chain Aa residue 912 VAL Chi-restraints excluded: chain Aa residue 914 THR Chi-restraints excluded: chain Aa residue 929 LEU Chi-restraints excluded: chain Aa residue 943 GLN Chi-restraints excluded: chain Aa residue 944 ASP Chi-restraints excluded: chain Aa residue 951 THR Chi-restraints excluded: chain Aa residue 1004 GLU Chi-restraints excluded: chain Aa residue 1016 VAL Chi-restraints excluded: chain Aa residue 1066 MET Chi-restraints excluded: chain Aa residue 1168 LEU Chi-restraints excluded: chain Aa residue 1181 LEU Chi-restraints excluded: chain Aa residue 1349 LEU Chi-restraints excluded: chain Aa residue 1363 VAL Chi-restraints excluded: chain Aa residue 1395 LEU Chi-restraints excluded: chain Aa residue 1400 VAL Chi-restraints excluded: chain Aa residue 1408 VAL Chi-restraints excluded: chain Aa residue 1480 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [18, 60, 120, 105, 112, 93, 73, 98, 32, 14, 92] chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 73 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Aa 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 522 GLN ** Aa 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa1035 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 = 0.3689 r_free = 0.3689 target = 0.136853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117280 restraints weight = 14674.332| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.32 r_work: 0.3339 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10352 Z= 0.128 Angle : 0.557 9.118 14054 Z= 0.283 Chirality : 0.042 0.206 1524 Planarity : 0.004 0.037 1781 Dihedral : 5.755 54.284 1425 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.19 % Allowed : 28.80 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.24), residues: 1249 helix: 1.69 (0.19), residues: 689 sheet: -1.70 (0.46), residues: 100 loop : -0.34 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAa1405 TYR 0.024 0.001 TYRAa 989 PHE 0.041 0.002 PHEAa1376 TRP 0.012 0.001 TRPAa 442 HIS 0.002 0.000 HISAa 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10349) covalent geometry : angle 0.55724 / 0.28 (14048) SS BOND : bond 0.00279 / 0.14 ( 3) SS BOND : angle 0.32165 / 0.15 ( 6) hydrogen bonds : bond 0.03471 / 2.21 ( 514) hydrogen bonds : angle 4.05399 / 2.87 ( 1494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.400 Fit side-chains REVERT: Aa 264 ARG cc_start: 0.6365 (OUTLIER) cc_final: 0.4654 (ppt170) REVERT: Aa 508 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6841 (mtt) REVERT: Aa 544 TYR cc_start: 0.8483 (t80) cc_final: 0.8256 (t80) REVERT: Aa 610 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7784 (t80) REVERT: Aa 611 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8893 (p) REVERT: Aa 657 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7337 (ttp) REVERT: Aa 705 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8580 (m-10) REVERT: Aa 765 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8393 (tt) REVERT: Aa 943 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7214 (mp10) REVERT: Aa 1004 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7866 (tp30) REVERT: Aa 1066 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7836 (mmt) REVERT: Aa 1147 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7522 (mm-30) REVERT: Aa 1148 GLU cc_start: 0.7716 (tp30) cc_final: 0.7491 (tp30) REVERT: Aa 1409 SER cc_start: 0.8767 (m) cc_final: 0.8360 (p) REVERT: Aa 1428 PHE cc_start: 0.8455 (t80) cc_final: 0.8255 (t80) REVERT: Aa 1476 ILE cc_start: 0.8110 (mt) cc_final: 0.7832 (mp) outliers start: 45 outliers final: 25 residues processed: 188 average time/residue: 0.3940 time to fit residues: 82.2763 Evaluate side-chains 186 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 123 ILE Chi-restraints excluded: chain Aa residue 202 VAL Chi-restraints excluded: chain Aa residue 264 ARG Chi-restraints excluded: chain Aa residue 348 SER Chi-restraints excluded: chain Aa residue 383 ILE Chi-restraints excluded: chain Aa residue 434 THR Chi-restraints excluded: chain Aa residue 508 MET Chi-restraints excluded: chain Aa residue 591 LEU Chi-restraints excluded: chain Aa residue 610 PHE Chi-restraints excluded: chain Aa residue 611 VAL Chi-restraints excluded: chain Aa residue 645 SER Chi-restraints excluded: chain Aa residue 649 VAL Chi-restraints excluded: chain Aa residue 657 MET Chi-restraints excluded: chain Aa residue 696 VAL Chi-restraints excluded: chain Aa residue 705 PHE Chi-restraints excluded: chain Aa residue 716 VAL Chi-restraints excluded: chain Aa residue 765 LEU Chi-restraints excluded: chain Aa residue 778 ILE Chi-restraints excluded: chain Aa residue 876 VAL Chi-restraints excluded: chain Aa residue 894 MET Chi-restraints excluded: chain Aa residue 905 LEU Chi-restraints excluded: chain Aa residue 912 VAL Chi-restraints excluded: chain Aa residue 914 THR Chi-restraints excluded: chain Aa residue 929 LEU Chi-restraints excluded: chain Aa residue 943 GLN Chi-restraints excluded: chain Aa residue 951 THR Chi-restraints excluded: chain Aa residue 1004 GLU Chi-restraints excluded: chain Aa residue 1016 VAL Chi-restraints excluded: chain Aa residue 1066 MET Chi-restraints excluded: chain Aa residue 1168 LEU Chi-restraints excluded: chain Aa residue 1181 LEU Chi-restraints excluded: chain Aa residue 1363 VAL Chi-restraints excluded: chain Aa residue 1395 LEU Chi-restraints excluded: chain Aa residue 1400 VAL Chi-restraints excluded: chain Aa residue 1408 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [1, 24, 31, 42, 53, 86, 83, 64, 14, 4, 55] chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Aa 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 522 GLN Aa 557 ASN Aa 609 ASN ** Aa1035 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 = 0.3674 r_free = 0.3674 target = 0.136139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.116615 restraints weight = 14558.768| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.31 r_work: 0.3341 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10352 Z= 0.132 Angle : 0.561 8.823 14054 Z= 0.285 Chirality : 0.042 0.192 1524 Planarity : 0.004 0.039 1781 Dihedral : 5.737 54.291 1425 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.63 % Allowed : 29.17 % Favored : 67.19 % 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: 0.95 (0.24), residues: 1249 helix: 1.70 (0.19), residues: 687 sheet: -1.79 (0.45), residues: 100 loop : -0.35 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAa1405 TYR 0.024 0.001 TYRAa 989 PHE 0.015 0.001 PHEAa 438 TRP 0.012 0.001 TRPAa 442 HIS 0.001 0.000 HISAa 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10349) covalent geometry : angle 0.56082 / 0.28 (14048) SS BOND : bond 0.00305 / 0.15 ( 3) SS BOND : angle 0.26361 / 0.12 ( 6) hydrogen bonds : bond 0.03426 / 2.18 ( 514) hydrogen bonds : angle 4.05464 / 2.86 ( 1494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.389 Fit side-chains REVERT: Aa 264 ARG cc_start: 0.6371 (OUTLIER) cc_final: 0.4649 (ppt170) REVERT: Aa 508 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6882 (mtt) REVERT: Aa 568 LEU cc_start: 0.8361 (tp) cc_final: 0.8141 (tt) REVERT: Aa 585 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8025 (mtt-85) REVERT: Aa 610 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7741 (t80) REVERT: Aa 611 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8861 (p) REVERT: Aa 657 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7339 (ttp) REVERT: Aa 705 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8541 (m-10) REVERT: Aa 765 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8375 (tt) REVERT: Aa 943 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: Aa 1004 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: Aa 1066 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7833 (mmt) REVERT: Aa 1090 ASN cc_start: 0.7907 (m110) cc_final: 0.7051 (t0) REVERT: Aa 1147 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7589 (tp30) REVERT: Aa 1148 GLU cc_start: 0.7708 (tp30) cc_final: 0.7493 (tp30) REVERT: Aa 1409 SER cc_start: 0.8759 (m) cc_final: 0.8357 (p) REVERT: Aa 1428 PHE cc_start: 0.8455 (t80) cc_final: 0.8254 (t80) REVERT: Aa 1476 ILE cc_start: 0.8145 (mt) cc_final: 0.7828 (mp) outliers start: 39 outliers final: 25 residues processed: 184 average time/residue: 0.3837 time to fit residues: 78.3753 Evaluate side-chains 187 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 123 ILE Chi-restraints excluded: chain Aa residue 202 VAL Chi-restraints excluded: chain Aa residue 264 ARG Chi-restraints excluded: chain Aa residue 298 ASP Chi-restraints excluded: chain Aa residue 348 SER Chi-restraints excluded: chain Aa residue 383 ILE Chi-restraints excluded: chain Aa residue 434 THR Chi-restraints excluded: chain Aa residue 508 MET Chi-restraints excluded: chain Aa residue 585 ARG Chi-restraints excluded: chain Aa residue 591 LEU Chi-restraints excluded: chain Aa residue 610 PHE Chi-restraints excluded: chain Aa residue 611 VAL Chi-restraints excluded: chain Aa residue 645 SER Chi-restraints excluded: chain Aa residue 649 VAL Chi-restraints excluded: chain Aa residue 657 MET Chi-restraints excluded: chain Aa residue 696 VAL Chi-restraints excluded: chain Aa residue 705 PHE Chi-restraints excluded: chain Aa residue 716 VAL Chi-restraints excluded: chain Aa residue 765 LEU Chi-restraints excluded: chain Aa residue 778 ILE Chi-restraints excluded: chain Aa residue 876 VAL Chi-restraints excluded: chain Aa residue 894 MET Chi-restraints excluded: chain Aa residue 905 LEU Chi-restraints excluded: chain Aa residue 912 VAL Chi-restraints excluded: chain Aa residue 914 THR Chi-restraints excluded: chain Aa residue 929 LEU Chi-restraints excluded: chain Aa residue 943 GLN Chi-restraints excluded: chain Aa residue 951 THR Chi-restraints excluded: chain Aa residue 1004 GLU Chi-restraints excluded: chain Aa residue 1016 VAL Chi-restraints excluded: chain Aa residue 1066 MET Chi-restraints excluded: chain Aa residue 1168 LEU Chi-restraints excluded: chain Aa residue 1181 LEU Chi-restraints excluded: chain Aa residue 1363 VAL Chi-restraints excluded: chain Aa residue 1395 LEU Chi-restraints excluded: chain Aa residue 1400 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [7, 90, 46, 74, 106, 22, 26, 5, 60, 120, 45] chunk 7 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 5 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Aa 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 522 GLN ** Aa1035 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 = 0.3676 r_free = 0.3676 target = 0.136315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116579 restraints weight = 14731.486| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.34 r_work: 0.3344 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10352 Z= 0.132 Angle : 0.569 9.077 14054 Z= 0.288 Chirality : 0.042 0.218 1524 Planarity : 0.004 0.041 1781 Dihedral : 5.693 54.294 1424 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.01 % Allowed : 28.89 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.24), residues: 1249 helix: 1.69 (0.19), residues: 687 sheet: -1.81 (0.45), residues: 100 loop : -0.36 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAa1405 TYR 0.025 0.001 TYRAa 989 PHE 0.040 0.002 PHEAa1376 TRP 0.014 0.001 TRPAa 861 HIS 0.002 0.000 HISAa 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10349) covalent geometry : angle 0.56904 / 0.29 (14048) SS BOND : bond 0.00307 / 0.15 ( 3) SS BOND : angle 0.31703 / 0.14 ( 6) hydrogen bonds : bond 0.03410 / 2.16 ( 514) hydrogen bonds : angle 4.04636 / 2.86 ( 1494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3064.68 seconds wall clock time: 53 minutes 3.11 seconds (3183.11 seconds total)