Starting phenix.real_space_refine on Tue May 13 00:21:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wi3_37556/05_2025/8wi3_37556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wi3_37556/05_2025/8wi3_37556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wi3_37556/05_2025/8wi3_37556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wi3_37556/05_2025/8wi3_37556.map" model { file = "/net/cci-nas-00/data/ceres_data/8wi3_37556/05_2025/8wi3_37556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wi3_37556/05_2025/8wi3_37556.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.124 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 6099 2.51 5 N 1616 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9489 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9489 Classifications: {'peptide': 1208} Link IDs: {'PTRANS': 35, 'TRANS': 1172} Chain breaks: 3 Time building chain proxies: 5.65, per 1000 atoms: 0.60 Number of scatterers: 9489 At special positions: 0 Unit cell: (77.4, 116.1, 159.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1716 8.00 N 1616 7.00 C 6099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.0 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 7 sheets defined 66.1% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.689A pdb=" N ALA A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 133 removed outlier: 3.894A pdb=" N VAL A 133 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 160 removed outlier: 3.965A pdb=" N ASN A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 4.154A pdb=" N VAL A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 193 removed outlier: 3.833A pdb=" N LEU A 179 " --> pdb=" O CYS A 175 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 210 removed outlier: 4.089A pdb=" N VAL A 201 " --> pdb=" O PRO A 197 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LYS A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 263 removed outlier: 3.647A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 293 removed outlier: 4.061A pdb=" N ARG A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 removed outlier: 4.300A pdb=" N VAL A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 321 through 361 Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.813A pdb=" N TYR A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 401 removed outlier: 3.867A pdb=" N SER A 378 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 423 removed outlier: 4.279A pdb=" N ILE A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 Processing helix chain 'A' and resid 445 through 448 Processing helix chain 'A' and resid 449 through 471 removed outlier: 3.598A pdb=" N SER A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 removed outlier: 3.592A pdb=" N LEU A 609 " --> pdb=" O ILE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 645 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 663 through 670 removed outlier: 3.676A pdb=" N ALA A 668 " --> pdb=" O ARG A 664 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 669 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 702 removed outlier: 3.814A pdb=" N ASP A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 728 Processing helix chain 'A' and resid 745 through 749 removed outlier: 3.659A pdb=" N VAL A 748 " --> pdb=" O GLN A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 774 Processing helix chain 'A' and resid 775 through 786 Processing helix chain 'A' and resid 842 through 854 removed outlier: 4.427A pdb=" N TYR A 846 " --> pdb=" O PRO A 842 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 886 removed outlier: 3.857A pdb=" N PHE A 859 " --> pdb=" O GLY A 855 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 884 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 885 " --> pdb=" O SER A 881 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN A 886 " --> pdb=" O TYR A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 954 removed outlier: 3.564A pdb=" N ALA A 915 " --> pdb=" O MET A 911 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 947 " --> pdb=" O ALA A 943 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS A 948 " --> pdb=" O SER A 944 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP A 949 " --> pdb=" O SER A 945 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.946A pdb=" N ASP A 980 " --> pdb=" O SER A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1011 removed outlier: 4.139A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A1011 " --> pdb=" O ILE A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1015 removed outlier: 3.845A pdb=" N LEU A1015 " --> pdb=" O PRO A1012 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1012 through 1015' Processing helix chain 'A' and resid 1018 through 1047 removed outlier: 4.264A pdb=" N ILE A1030 " --> pdb=" O SER A1026 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL A1031 " --> pdb=" O VAL A1027 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A1042 " --> pdb=" O GLU A1038 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1059 removed outlier: 3.852A pdb=" N LEU A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1067 removed outlier: 3.871A pdb=" N ILE A1064 " --> pdb=" O GLY A1060 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A1067 " --> pdb=" O THR A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1120 Proline residue: A1087 - end of helix removed outlier: 3.711A pdb=" N MET A1120 " --> pdb=" O MET A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1138 removed outlier: 3.626A pdb=" N ALA A1129 " --> pdb=" O PRO A1125 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN A1138 " --> pdb=" O SER A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1156 removed outlier: 3.659A pdb=" N ARG A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1169 Processing helix chain 'A' and resid 1232 through 1241 removed outlier: 4.131A pdb=" N LEU A1236 " --> pdb=" O GLY A1232 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY A1237 " --> pdb=" O LYS A1233 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A1241 " --> pdb=" O GLY A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1268 Processing helix chain 'A' and resid 1284 through 1289 Processing helix chain 'A' and resid 1295 through 1306 removed outlier: 3.666A pdb=" N ILE A1299 " --> pdb=" O THR A1295 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A1306 " --> pdb=" O ALA A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1315 removed outlier: 3.504A pdb=" N ILE A1312 " --> pdb=" O MET A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1320 Processing helix chain 'A' and resid 1324 through 1328 removed outlier: 3.532A pdb=" N ASP A1328 " --> pdb=" O GLU A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1347 removed outlier: 3.916A pdb=" N ARG A1346 " --> pdb=" O ARG A1342 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS A1347 " --> pdb=" O ALA A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1376 Processing helix chain 'A' and resid 1387 through 1393 removed outlier: 3.901A pdb=" N VAL A1391 " --> pdb=" O ARG A1387 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY A1393 " --> pdb=" O HIS A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1417 Processing helix chain 'A' and resid 1420 through 1435 removed outlier: 3.559A pdb=" N LYS A1432 " --> pdb=" O ALA A1428 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL A1433 " --> pdb=" O ALA A1429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 581 through 586 removed outlier: 3.522A pdb=" N ILE A 581 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 495 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU A 583 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS A 493 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE A 585 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU A 491 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 620 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS A 493 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 618 " --> pdb=" O LYS A 493 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 575 through 576 removed outlier: 3.955A pdb=" N ALA A 498 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR A 613 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 625 through 628 removed outlier: 6.023A pdb=" N ALA A 626 " --> pdb=" O ILE A 707 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP A 709 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 628 " --> pdb=" O ASP A 709 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR A 706 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL A 740 " --> pdb=" O TYR A 706 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 708 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU A 752 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY A 765 " --> pdb=" O VAL A 753 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 755 " --> pdb=" O GLU A 763 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU A 763 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS A 757 " --> pdb=" O ILE A 761 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE A 761 " --> pdb=" O LYS A 757 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 892 through 893 Processing sheet with id=AA5, first strand: chain 'A' and resid 1216 through 1217 removed outlier: 4.371A pdb=" N ALA A1198 " --> pdb=" O GLY A1248 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY A1248 " --> pdb=" O ALA A1198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1271 through 1273 removed outlier: 3.546A pdb=" N SER A1271 " --> pdb=" O ILE A1350 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A1354 " --> pdb=" O ILE A1273 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS A1222 " --> pdb=" O ARG A1396 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N MET A1398 " --> pdb=" O LYS A1222 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY A1224 " --> pdb=" O MET A1398 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU A1400 " --> pdb=" O GLY A1224 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL A1226 " --> pdb=" O LEU A1400 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE A1397 " --> pdb=" O PHE A1408 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE A1408 " --> pdb=" O ILE A1397 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A1399 " --> pdb=" O VAL A1406 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1282 through 1283 559 hydrogen bonds defined for protein. 1632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3059 1.34 - 1.46: 2033 1.46 - 1.58: 4481 1.58 - 1.70: 1 1.70 - 1.82: 98 Bond restraints: 9672 Sorted by residual: bond pdb=" CB PRO A1277 " pdb=" CG PRO A1277 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.45e+00 bond pdb=" C ALA A 406 " pdb=" N PRO A 407 " ideal model delta sigma weight residual 1.335 1.361 -0.027 1.28e-02 6.10e+03 4.37e+00 bond pdb=" CA ALA A1086 " pdb=" C ALA A1086 " ideal model delta sigma weight residual 1.520 1.546 -0.025 1.23e-02 6.61e+03 4.22e+00 bond pdb=" C ASP A1082 " pdb=" O ASP A1082 " ideal model delta sigma weight residual 1.237 1.257 -0.021 1.17e-02 7.31e+03 3.14e+00 bond pdb=" C TRP A1097 " pdb=" O TRP A1097 " ideal model delta sigma weight residual 1.236 1.254 -0.018 1.15e-02 7.56e+03 2.49e+00 ... (remaining 9667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 12994 3.18 - 6.37: 90 6.37 - 9.55: 5 9.55 - 12.74: 1 12.74 - 15.92: 1 Bond angle restraints: 13091 Sorted by residual: angle pdb=" N ILE A 971 " pdb=" CA ILE A 971 " pdb=" C ILE A 971 " ideal model delta sigma weight residual 112.96 108.20 4.76 1.00e+00 1.00e+00 2.26e+01 angle pdb=" CA LEU A 956 " pdb=" CB LEU A 956 " pdb=" CG LEU A 956 " ideal model delta sigma weight residual 116.30 132.22 -15.92 3.50e+00 8.16e-02 2.07e+01 angle pdb=" C ASP A 983 " pdb=" N VAL A 984 " pdb=" CA VAL A 984 " ideal model delta sigma weight residual 123.08 118.61 4.47 1.01e+00 9.80e-01 1.96e+01 angle pdb=" CA PRO A1277 " pdb=" N PRO A1277 " pdb=" CD PRO A1277 " ideal model delta sigma weight residual 112.00 107.04 4.96 1.40e+00 5.10e-01 1.26e+01 angle pdb=" N ILE A 955 " pdb=" CA ILE A 955 " pdb=" C ILE A 955 " ideal model delta sigma weight residual 111.81 108.77 3.04 8.60e-01 1.35e+00 1.25e+01 ... (remaining 13086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4931 17.97 - 35.95: 692 35.95 - 53.92: 144 53.92 - 71.90: 27 71.90 - 89.87: 11 Dihedral angle restraints: 5805 sinusoidal: 2299 harmonic: 3506 Sorted by residual: dihedral pdb=" CA ASN A1068 " pdb=" C ASN A1068 " pdb=" N LYS A1069 " pdb=" CA LYS A1069 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA TYR A 364 " pdb=" C TYR A 364 " pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta harmonic sigma weight residual -180.00 -157.08 -22.92 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA THR A 363 " pdb=" C THR A 363 " pdb=" N TYR A 364 " pdb=" CA TYR A 364 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 5802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 992 0.032 - 0.065: 387 0.065 - 0.097: 90 0.097 - 0.129: 53 0.129 - 0.161: 10 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CA TYR A 330 " pdb=" N TYR A 330 " pdb=" C TYR A 330 " pdb=" CB TYR A 330 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CG LEU A 715 " pdb=" CB LEU A 715 " pdb=" CD1 LEU A 715 " pdb=" CD2 LEU A 715 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CB ILE A 277 " pdb=" CA ILE A 277 " pdb=" CG1 ILE A 277 " pdb=" CG2 ILE A 277 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 1529 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 664 " 0.050 5.00e-02 4.00e+02 7.50e-02 9.01e+00 pdb=" N PRO A 665 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 665 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 665 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 958 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO A 959 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 959 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 959 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 300 " 0.042 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO A 301 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " 0.036 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 586 2.73 - 3.27: 9299 3.27 - 3.81: 14563 3.81 - 4.36: 15284 4.36 - 4.90: 27669 Nonbonded interactions: 67401 Sorted by model distance: nonbonded pdb=" NZ LYS A 261 " pdb=" OE1 GLU A 475 " model vdw 2.187 3.120 nonbonded pdb=" OG1 THR A1295 " pdb=" OE1 GLN A1298 " model vdw 2.232 3.040 nonbonded pdb=" ND1 HIS A 97 " pdb=" OD1 ASN A 103 " model vdw 2.259 3.120 nonbonded pdb=" O ALA A 698 " pdb=" OG SER A 701 " model vdw 2.287 3.040 nonbonded pdb=" OG SER A 944 " pdb=" OD1 ASP A 983 " model vdw 2.320 3.040 ... (remaining 67396 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 24.070 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 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 : 0.004 0.105 9672 Z= 0.219 Angle : 0.683 15.924 13091 Z= 0.389 Chirality : 0.040 0.161 1532 Planarity : 0.005 0.075 1640 Dihedral : 17.114 89.873 3533 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.58 % Favored : 93.33 % Rotamer: Outliers : 0.38 % Allowed : 25.10 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1200 helix: 2.02 (0.19), residues: 703 sheet: 2.56 (0.67), residues: 64 loop : -1.92 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1097 HIS 0.006 0.001 HIS A 722 PHE 0.020 0.002 PHE A 434 TYR 0.019 0.002 TYR A 918 ARG 0.003 0.000 ARG A 178 Details of bonding type rmsd hydrogen bonds : bond 0.18152 ( 559) hydrogen bonds : angle 5.28753 ( 1632) covalent geometry : bond 0.00425 ( 9672) covalent geometry : angle 0.68345 (13091) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 1.102 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 113 average time/residue: 0.2104 time to fit residues: 34.0315 Evaluate side-chains 113 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1205 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.240544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.185493 restraints weight = 11429.413| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 3.05 r_work: 0.3829 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9672 Z= 0.182 Angle : 0.572 14.325 13091 Z= 0.306 Chirality : 0.039 0.141 1532 Planarity : 0.004 0.064 1640 Dihedral : 4.356 30.042 1304 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.17 % Favored : 93.75 % Rotamer: Outliers : 2.31 % Allowed : 23.65 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1200 helix: 2.08 (0.19), residues: 716 sheet: 2.39 (0.65), residues: 69 loop : -2.04 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1097 HIS 0.004 0.001 HIS A 767 PHE 0.014 0.001 PHE A 434 TYR 0.021 0.001 TYR A 918 ARG 0.002 0.000 ARG A 178 Details of bonding type rmsd hydrogen bonds : bond 0.11146 ( 559) hydrogen bonds : angle 4.50727 ( 1632) covalent geometry : bond 0.00334 ( 9672) covalent geometry : angle 0.57157 (13091) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.055 Fit side-chains REVERT: A 127 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: A 601 LYS cc_start: 0.6849 (OUTLIER) cc_final: 0.6428 (mttt) REVERT: A 612 MET cc_start: 0.6697 (tpp) cc_final: 0.6225 (tpp) REVERT: A 674 ASP cc_start: 0.7908 (p0) cc_final: 0.7660 (p0) REVERT: A 712 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7303 (pt) REVERT: A 918 TYR cc_start: 0.6360 (OUTLIER) cc_final: 0.5138 (m-80) REVERT: A 979 MET cc_start: 0.7957 (mmm) cc_final: 0.7720 (mmm) REVERT: A 1113 THR cc_start: 0.7215 (t) cc_final: 0.6962 (t) REVERT: A 1324 MET cc_start: 0.7933 (ttm) cc_final: 0.7701 (mmm) REVERT: A 1325 GLU cc_start: 0.7683 (pt0) cc_final: 0.7236 (pt0) REVERT: A 1360 MET cc_start: 0.1321 (OUTLIER) cc_final: 0.0717 (ppp) outliers start: 24 outliers final: 9 residues processed: 136 average time/residue: 0.1936 time to fit residues: 38.5020 Evaluate side-chains 129 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1360 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 105 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 56 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.243269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.188727 restraints weight = 11557.821| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 3.01 r_work: 0.3879 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9672 Z= 0.166 Angle : 0.548 12.471 13091 Z= 0.289 Chirality : 0.039 0.156 1532 Planarity : 0.004 0.062 1640 Dihedral : 4.210 27.274 1303 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.08 % Favored : 93.75 % Rotamer: Outliers : 3.27 % Allowed : 24.42 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1200 helix: 2.11 (0.19), residues: 723 sheet: 2.39 (0.64), residues: 69 loop : -1.99 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1097 HIS 0.003 0.001 HIS A 767 PHE 0.012 0.001 PHE A 434 TYR 0.017 0.001 TYR A 918 ARG 0.004 0.000 ARG A1335 Details of bonding type rmsd hydrogen bonds : bond 0.10171 ( 559) hydrogen bonds : angle 4.25738 ( 1632) covalent geometry : bond 0.00292 ( 9672) covalent geometry : angle 0.54752 (13091) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.981 Fit side-chains REVERT: A 320 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.6461 (t80) REVERT: A 601 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6209 (mttt) REVERT: A 674 ASP cc_start: 0.7951 (p0) cc_final: 0.7676 (p0) REVERT: A 712 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7233 (pt) REVERT: A 918 TYR cc_start: 0.6334 (OUTLIER) cc_final: 0.5073 (m-80) REVERT: A 949 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.6730 (t0) REVERT: A 960 MET cc_start: 0.5659 (pmm) cc_final: 0.5106 (tpt) REVERT: A 979 MET cc_start: 0.7996 (mmm) cc_final: 0.7685 (mmm) REVERT: A 1325 GLU cc_start: 0.7849 (pt0) cc_final: 0.7444 (pt0) REVERT: A 1360 MET cc_start: 0.1353 (OUTLIER) cc_final: 0.0676 (ppp) outliers start: 34 outliers final: 18 residues processed: 142 average time/residue: 0.1769 time to fit residues: 37.0467 Evaluate side-chains 140 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1283 THR Chi-restraints excluded: chain A residue 1360 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 97 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 101 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1298 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.239855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.185209 restraints weight = 11482.692| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.96 r_work: 0.3829 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9672 Z= 0.180 Angle : 0.554 11.521 13091 Z= 0.295 Chirality : 0.039 0.146 1532 Planarity : 0.004 0.062 1640 Dihedral : 4.171 25.569 1303 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.58 % Favored : 93.33 % Rotamer: Outliers : 3.85 % Allowed : 24.13 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1200 helix: 2.08 (0.19), residues: 724 sheet: 2.36 (0.64), residues: 69 loop : -1.99 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1097 HIS 0.016 0.001 HIS A 722 PHE 0.017 0.001 PHE A 434 TYR 0.022 0.001 TYR A 918 ARG 0.002 0.000 ARG A 974 Details of bonding type rmsd hydrogen bonds : bond 0.11051 ( 559) hydrogen bonds : angle 4.26472 ( 1632) covalent geometry : bond 0.00335 ( 9672) covalent geometry : angle 0.55448 (13091) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 1.082 Fit side-chains REVERT: A 127 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: A 320 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6666 (t80) REVERT: A 367 PHE cc_start: 0.8576 (t80) cc_final: 0.8272 (t80) REVERT: A 422 MET cc_start: 0.8414 (mmm) cc_final: 0.7912 (mmm) REVERT: A 601 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6498 (mttm) REVERT: A 674 ASP cc_start: 0.7999 (p0) cc_final: 0.7724 (p0) REVERT: A 712 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7216 (pt) REVERT: A 918 TYR cc_start: 0.6708 (OUTLIER) cc_final: 0.5420 (m-80) REVERT: A 949 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.6758 (t0) REVERT: A 960 MET cc_start: 0.5943 (pmm) cc_final: 0.5164 (tpt) REVERT: A 1298 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7085 (mp10) REVERT: A 1360 MET cc_start: 0.1274 (OUTLIER) cc_final: 0.0775 (ppp) REVERT: A 1398 MET cc_start: 0.3831 (tpp) cc_final: 0.2913 (ttm) REVERT: A 1406 VAL cc_start: 0.5178 (OUTLIER) cc_final: 0.4939 (m) outliers start: 40 outliers final: 25 residues processed: 151 average time/residue: 0.2023 time to fit residues: 45.0085 Evaluate side-chains 153 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1283 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1298 GLN Chi-restraints excluded: chain A residue 1360 MET Chi-restraints excluded: chain A residue 1406 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.238796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.184668 restraints weight = 11476.636| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 3.19 r_work: 0.3800 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9672 Z= 0.186 Angle : 0.569 14.065 13091 Z= 0.300 Chirality : 0.039 0.144 1532 Planarity : 0.004 0.062 1640 Dihedral : 4.189 25.470 1303 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.42 % Favored : 93.42 % Rotamer: Outliers : 4.52 % Allowed : 24.71 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1200 helix: 2.03 (0.19), residues: 725 sheet: 2.30 (0.64), residues: 69 loop : -1.99 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1097 HIS 0.022 0.001 HIS A 722 PHE 0.015 0.001 PHE A 434 TYR 0.022 0.001 TYR A 918 ARG 0.002 0.000 ARG A 974 Details of bonding type rmsd hydrogen bonds : bond 0.11256 ( 559) hydrogen bonds : angle 4.28593 ( 1632) covalent geometry : bond 0.00357 ( 9672) covalent geometry : angle 0.56905 (13091) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 1.135 Fit side-chains REVERT: A 127 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7265 (pm20) REVERT: A 320 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6705 (t80) REVERT: A 367 PHE cc_start: 0.8525 (t80) cc_final: 0.8233 (t80) REVERT: A 478 MET cc_start: 0.5454 (tpp) cc_final: 0.4374 (ttt) REVERT: A 601 LYS cc_start: 0.6721 (OUTLIER) cc_final: 0.6325 (mttt) REVERT: A 674 ASP cc_start: 0.7966 (p0) cc_final: 0.7691 (p0) REVERT: A 907 ASP cc_start: 0.8837 (t0) cc_final: 0.8440 (t0) REVERT: A 918 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.5365 (m-80) REVERT: A 949 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.6784 (t0) REVERT: A 960 MET cc_start: 0.5956 (pmm) cc_final: 0.5199 (tpt) REVERT: A 1271 SER cc_start: 0.8450 (t) cc_final: 0.8209 (p) REVERT: A 1293 GLN cc_start: 0.8414 (mt0) cc_final: 0.8169 (mm110) REVERT: A 1298 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7200 (pm20) REVERT: A 1355 GLU cc_start: 0.5804 (tm-30) cc_final: 0.5355 (tm-30) REVERT: A 1360 MET cc_start: 0.0839 (OUTLIER) cc_final: 0.0337 (ppp) REVERT: A 1398 MET cc_start: 0.4170 (tpp) cc_final: 0.3139 (ttm) REVERT: A 1406 VAL cc_start: 0.5242 (OUTLIER) cc_final: 0.5004 (m) outliers start: 47 outliers final: 32 residues processed: 158 average time/residue: 0.1894 time to fit residues: 44.1591 Evaluate side-chains 162 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1283 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1298 GLN Chi-restraints excluded: chain A residue 1360 MET Chi-restraints excluded: chain A residue 1406 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS ** A 722 HIS ** 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 = 0.4720 r_free = 0.4720 target = 0.241642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.187435 restraints weight = 11500.082| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 3.17 r_work: 0.3840 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9672 Z= 0.166 Angle : 0.538 9.327 13091 Z= 0.286 Chirality : 0.039 0.152 1532 Planarity : 0.004 0.062 1640 Dihedral : 4.110 25.722 1301 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.42 % Favored : 93.42 % Rotamer: Outliers : 4.62 % Allowed : 25.00 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1200 helix: 2.15 (0.19), residues: 725 sheet: 2.36 (0.64), residues: 69 loop : -1.97 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1097 HIS 0.021 0.001 HIS A 722 PHE 0.013 0.001 PHE A 434 TYR 0.018 0.001 TYR A 918 ARG 0.002 0.000 ARG A1335 Details of bonding type rmsd hydrogen bonds : bond 0.10290 ( 559) hydrogen bonds : angle 4.15893 ( 1632) covalent geometry : bond 0.00295 ( 9672) covalent geometry : angle 0.53800 (13091) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 1.079 Fit side-chains REVERT: A 127 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: A 260 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6797 (tttm) REVERT: A 320 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6731 (t80) REVERT: A 358 MET cc_start: 0.6118 (tpt) cc_final: 0.5590 (tpt) REVERT: A 482 LYS cc_start: 0.8017 (tppt) cc_final: 0.7782 (tppt) REVERT: A 601 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6437 (mttt) REVERT: A 907 ASP cc_start: 0.8863 (t0) cc_final: 0.8471 (t0) REVERT: A 918 TYR cc_start: 0.6644 (OUTLIER) cc_final: 0.5343 (m-80) REVERT: A 949 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.6738 (t0) REVERT: A 960 MET cc_start: 0.5844 (pmm) cc_final: 0.5156 (tpt) REVERT: A 979 MET cc_start: 0.8078 (mmm) cc_final: 0.7683 (mmm) REVERT: A 1116 MET cc_start: 0.7162 (tpp) cc_final: 0.6417 (tpp) REVERT: A 1271 SER cc_start: 0.8288 (t) cc_final: 0.8069 (p) REVERT: A 1298 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7418 (mp10) REVERT: A 1325 GLU cc_start: 0.7840 (pt0) cc_final: 0.7406 (pm20) REVERT: A 1355 GLU cc_start: 0.5988 (tm-30) cc_final: 0.5415 (tm-30) REVERT: A 1360 MET cc_start: 0.1170 (OUTLIER) cc_final: 0.0597 (ppp) REVERT: A 1398 MET cc_start: 0.4160 (tpp) cc_final: 0.3160 (ttm) REVERT: A 1406 VAL cc_start: 0.5614 (OUTLIER) cc_final: 0.5410 (m) outliers start: 48 outliers final: 29 residues processed: 161 average time/residue: 0.1842 time to fit residues: 43.5712 Evaluate side-chains 161 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1298 GLN Chi-restraints excluded: chain A residue 1360 MET Chi-restraints excluded: chain A residue 1406 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 0.0270 chunk 68 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 20 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.234084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.199246 restraints weight = 10703.524| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.13 r_work: 0.3814 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9672 Z= 0.165 Angle : 0.549 9.051 13091 Z= 0.288 Chirality : 0.039 0.209 1532 Planarity : 0.004 0.081 1640 Dihedral : 4.089 25.832 1301 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.33 % Favored : 93.50 % Rotamer: Outliers : 4.71 % Allowed : 25.10 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1200 helix: 2.20 (0.19), residues: 725 sheet: 2.33 (0.64), residues: 69 loop : -1.99 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1097 HIS 0.020 0.001 HIS A 722 PHE 0.013 0.001 PHE A 434 TYR 0.019 0.001 TYR A 918 ARG 0.002 0.000 ARG A 974 Details of bonding type rmsd hydrogen bonds : bond 0.10049 ( 559) hydrogen bonds : angle 4.10484 ( 1632) covalent geometry : bond 0.00293 ( 9672) covalent geometry : angle 0.54948 (13091) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 0.975 Fit side-chains REVERT: A 127 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.6954 (pm20) REVERT: A 260 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6716 (tttm) REVERT: A 320 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6810 (t80) REVERT: A 478 MET cc_start: 0.5173 (tpp) cc_final: 0.4417 (ttt) REVERT: A 601 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.6002 (mttt) REVERT: A 907 ASP cc_start: 0.8445 (t0) cc_final: 0.8160 (t0) REVERT: A 918 TYR cc_start: 0.6328 (OUTLIER) cc_final: 0.5117 (m-80) REVERT: A 949 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.6885 (t0) REVERT: A 960 MET cc_start: 0.5516 (pmm) cc_final: 0.5232 (tpt) REVERT: A 974 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6041 (ttp-110) REVERT: A 1271 SER cc_start: 0.7264 (t) cc_final: 0.7043 (m) REVERT: A 1360 MET cc_start: 0.1395 (OUTLIER) cc_final: 0.1150 (ppp) REVERT: A 1398 MET cc_start: 0.5357 (tpp) cc_final: 0.3956 (ttm) outliers start: 49 outliers final: 30 residues processed: 163 average time/residue: 0.1910 time to fit residues: 45.3609 Evaluate side-chains 163 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 974 ARG Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1360 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 116 optimal weight: 0.2980 chunk 40 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.237088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.203030 restraints weight = 10859.035| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 1.80 r_work: 0.3894 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9672 Z= 0.155 Angle : 0.555 9.328 13091 Z= 0.289 Chirality : 0.039 0.203 1532 Planarity : 0.004 0.072 1640 Dihedral : 4.026 25.922 1300 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.42 % Favored : 93.42 % Rotamer: Outliers : 3.56 % Allowed : 25.87 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1200 helix: 2.24 (0.19), residues: 725 sheet: 2.56 (0.64), residues: 68 loop : -1.94 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1097 HIS 0.021 0.001 HIS A 722 PHE 0.011 0.001 PHE A 434 TYR 0.017 0.001 TYR A 918 ARG 0.002 0.000 ARG A1346 Details of bonding type rmsd hydrogen bonds : bond 0.09286 ( 559) hydrogen bonds : angle 4.04925 ( 1632) covalent geometry : bond 0.00266 ( 9672) covalent geometry : angle 0.55526 (13091) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 1.010 Fit side-chains REVERT: A 127 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: A 320 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.6644 (t80) REVERT: A 478 MET cc_start: 0.4995 (tpp) cc_final: 0.4056 (ttt) REVERT: A 601 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.5890 (mttt) REVERT: A 907 ASP cc_start: 0.8380 (t0) cc_final: 0.8086 (t0) REVERT: A 918 TYR cc_start: 0.6023 (OUTLIER) cc_final: 0.4858 (m-80) REVERT: A 949 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.6725 (t0) REVERT: A 960 MET cc_start: 0.5347 (pmm) cc_final: 0.5058 (tpt) REVERT: A 974 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6028 (ttp-110) REVERT: A 979 MET cc_start: 0.8244 (mmm) cc_final: 0.8015 (mmm) REVERT: A 1360 MET cc_start: 0.1095 (OUTLIER) cc_final: 0.0785 (ppp) REVERT: A 1365 ASP cc_start: 0.3674 (t0) cc_final: 0.3423 (t0) REVERT: A 1398 MET cc_start: 0.5775 (tpp) cc_final: 0.3957 (ttp) outliers start: 37 outliers final: 26 residues processed: 154 average time/residue: 0.1878 time to fit residues: 42.0916 Evaluate side-chains 157 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 974 ARG Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1360 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 18 optimal weight: 0.0050 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.233242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.196332 restraints weight = 10621.318| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.15 r_work: 0.3763 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9672 Z= 0.177 Angle : 0.579 12.154 13091 Z= 0.302 Chirality : 0.040 0.191 1532 Planarity : 0.004 0.070 1640 Dihedral : 4.036 25.786 1300 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.08 % Favored : 92.75 % Rotamer: Outliers : 4.04 % Allowed : 25.38 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1200 helix: 2.15 (0.19), residues: 725 sheet: 2.55 (0.65), residues: 68 loop : -1.97 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1097 HIS 0.022 0.001 HIS A 722 PHE 0.016 0.001 PHE A 434 TYR 0.022 0.001 TYR A 918 ARG 0.002 0.000 ARG A 974 Details of bonding type rmsd hydrogen bonds : bond 0.10597 ( 559) hydrogen bonds : angle 4.18062 ( 1632) covalent geometry : bond 0.00338 ( 9672) covalent geometry : angle 0.57925 (13091) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 1.089 Fit side-chains REVERT: A 127 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7051 (pm20) REVERT: A 260 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6828 (tttm) REVERT: A 320 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6935 (t80) REVERT: A 907 ASP cc_start: 0.8568 (t0) cc_final: 0.8289 (t0) REVERT: A 918 TYR cc_start: 0.6329 (OUTLIER) cc_final: 0.5116 (m-80) REVERT: A 949 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.6898 (t0) REVERT: A 974 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6084 (ttp-110) REVERT: A 1271 SER cc_start: 0.7375 (t) cc_final: 0.7124 (m) REVERT: A 1293 GLN cc_start: 0.8435 (mm110) cc_final: 0.8018 (mt0) outliers start: 42 outliers final: 30 residues processed: 154 average time/residue: 0.1941 time to fit residues: 43.4016 Evaluate side-chains 158 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 974 ARG Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1281 SER Chi-restraints excluded: chain A residue 1344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.235448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.201859 restraints weight = 10777.043| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 1.97 r_work: 0.3837 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9672 Z= 0.163 Angle : 0.561 9.312 13091 Z= 0.292 Chirality : 0.039 0.176 1532 Planarity : 0.004 0.067 1640 Dihedral : 4.023 25.743 1300 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.58 % Favored : 93.25 % Rotamer: Outliers : 3.37 % Allowed : 25.96 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1200 helix: 2.23 (0.19), residues: 725 sheet: 2.68 (0.66), residues: 68 loop : -1.96 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1097 HIS 0.023 0.001 HIS A 722 PHE 0.012 0.001 PHE A 434 TYR 0.018 0.001 TYR A 918 ARG 0.003 0.000 ARG A1346 Details of bonding type rmsd hydrogen bonds : bond 0.09843 ( 559) hydrogen bonds : angle 4.08945 ( 1632) covalent geometry : bond 0.00294 ( 9672) covalent geometry : angle 0.56106 (13091) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 1.027 Fit side-chains REVERT: A 127 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: A 320 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6703 (t80) REVERT: A 478 MET cc_start: 0.5237 (tpp) cc_final: 0.4429 (ttt) REVERT: A 907 ASP cc_start: 0.8521 (t0) cc_final: 0.8246 (t0) REVERT: A 918 TYR cc_start: 0.6156 (OUTLIER) cc_final: 0.4956 (m-80) REVERT: A 949 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.6753 (t0) REVERT: A 974 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6109 (ttp-110) REVERT: A 979 MET cc_start: 0.8275 (mmm) cc_final: 0.8041 (mmm) REVERT: A 1271 SER cc_start: 0.7262 (t) cc_final: 0.7056 (m) REVERT: A 1293 GLN cc_start: 0.8367 (mm110) cc_final: 0.7951 (mt0) REVERT: A 1365 ASP cc_start: 0.4276 (t0) cc_final: 0.4041 (t0) REVERT: A 1398 MET cc_start: 0.5631 (tpp) cc_final: 0.5301 (mmt) outliers start: 35 outliers final: 28 residues processed: 151 average time/residue: 0.1858 time to fit residues: 41.1218 Evaluate side-chains 157 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 974 ARG Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1281 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.232089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.179468 restraints weight = 10601.997| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 5.42 r_work: 0.3589 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9672 Z= 0.184 Angle : 0.619 17.664 13091 Z= 0.313 Chirality : 0.040 0.173 1532 Planarity : 0.004 0.066 1640 Dihedral : 4.060 25.758 1300 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.17 % Favored : 92.67 % Rotamer: Outliers : 3.94 % Allowed : 25.10 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1200 helix: 2.12 (0.19), residues: 723 sheet: 3.00 (0.66), residues: 62 loop : -1.94 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1097 HIS 0.022 0.001 HIS A 722 PHE 0.016 0.001 PHE A 434 TYR 0.022 0.001 TYR A 918 ARG 0.002 0.000 ARG A 974 Details of bonding type rmsd hydrogen bonds : bond 0.10911 ( 559) hydrogen bonds : angle 4.23165 ( 1632) covalent geometry : bond 0.00357 ( 9672) covalent geometry : angle 0.61861 (13091) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4432.56 seconds wall clock time: 77 minutes 28.42 seconds (4648.42 seconds total)