Starting phenix.real_space_refine on Sun Dec 29 01:02:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pmj_17761/12_2024/8pmj_17761.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pmj_17761/12_2024/8pmj_17761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pmj_17761/12_2024/8pmj_17761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pmj_17761/12_2024/8pmj_17761.map" model { file = "/net/cci-nas-00/data/ceres_data/8pmj_17761/12_2024/8pmj_17761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pmj_17761/12_2024/8pmj_17761.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians V 1 8.30 5 P 5 5.49 5 Mg 2 5.21 5 S 52 5.16 5 C 5774 2.51 5 N 1503 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8985 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8805 Classifications: {'peptide': 1133} Link IDs: {'PTRANS': 32, 'TRANS': 1100} Chain breaks: 4 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 180 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'CLR': 4, 'VO4': 1} Classifications: {'undetermined': 9, 'water': 3} Link IDs: {None: 11} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N VAL A 248 " occ=0.96 ... (5 atoms not shown) pdb=" CG2 VAL A 248 " occ=0.68 Time building chain proxies: 6.03, per 1000 atoms: 0.67 Number of scatterers: 8985 At special positions: 0 Unit cell: (104.94, 100.98, 127.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 S 52 16.00 P 5 15.00 Mg 2 11.99 O 1648 8.00 N 1503 7.00 C 5774 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: 2.58 Conformation dependent library (CDL) restraints added in 1.1 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 70.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.673A pdb=" N PHE A 51 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 52 " --> pdb=" O GLN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 100 removed outlier: 4.330A pdb=" N GLN A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Proline residue: A 77 - end of helix removed outlier: 3.637A pdb=" N ASP A 88 " --> pdb=" O GLY A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 183 removed outlier: 3.568A pdb=" N ARG A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 removed outlier: 3.747A pdb=" N PHE A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 214 removed outlier: 4.772A pdb=" N ILE A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 237 removed outlier: 3.696A pdb=" N GLY A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 287 removed outlier: 4.345A pdb=" N ILE A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Proline residue: A 250 - end of helix removed outlier: 3.807A pdb=" N VAL A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 296 through 344 removed outlier: 3.708A pdb=" N PHE A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 326 " --> pdb=" O MET A 322 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 removed outlier: 3.537A pdb=" N VAL A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 398 removed outlier: 3.509A pdb=" N LEU A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 469 removed outlier: 3.723A pdb=" N LEU A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 490 through 497 Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 537 through 543 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 560 through 574 Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.575A pdb=" N VAL A 600 " --> pdb=" O MET A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 739 through 748 Processing helix chain 'A' and resid 751 through 781 removed outlier: 4.005A pdb=" N THR A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) Proline residue: A 770 - end of helix removed outlier: 3.745A pdb=" N ALA A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 841 removed outlier: 3.661A pdb=" N ASN A 796 " --> pdb=" O ARG A 792 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 809 " --> pdb=" O MET A 805 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 821 " --> pdb=" O GLY A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.561A pdb=" N PHE A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 852 Processing helix chain 'A' and resid 853 through 873 removed outlier: 4.419A pdb=" N ALA A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 895 Processing helix chain 'A' and resid 897 through 908 removed outlier: 4.063A pdb=" N VAL A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 907 " --> pdb=" O VAL A 903 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 908 " --> pdb=" O ILE A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 946 removed outlier: 3.588A pdb=" N ALA A 912 " --> pdb=" O PHE A 908 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY A 924 " --> pdb=" O ARG A 920 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE A 925 " --> pdb=" O MET A 921 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 928 " --> pdb=" O GLY A 924 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN A 931 " --> pdb=" O SER A 927 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 932 " --> pdb=" O ARG A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 954 Processing helix chain 'A' and resid 955 through 1010 removed outlier: 4.511A pdb=" N LYS A 969 " --> pdb=" O THR A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix removed outlier: 3.991A pdb=" N THR A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 975 " --> pdb=" O PHE A 971 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN A 976 " --> pdb=" O LYS A 972 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 989 " --> pdb=" O PHE A 985 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1028 removed outlier: 4.091A pdb=" N VAL A1017 " --> pdb=" O HIS A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1039 removed outlier: 3.569A pdb=" N GLY A1032 " --> pdb=" O THR A1029 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A1034 " --> pdb=" O LEU A1031 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE A1035 " --> pdb=" O GLY A1032 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A1038 " --> pdb=" O PHE A1035 " (cutoff:3.500A) Proline residue: A1039 - end of helix Processing helix chain 'A' and resid 1040 through 1056 Processing helix chain 'A' and resid 1118 through 1127 removed outlier: 3.565A pdb=" N ILE A1123 " --> pdb=" O LYS A1119 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1126 " --> pdb=" O SER A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1147 No H-bonds generated for 'chain 'A' and resid 1145 through 1147' Processing helix chain 'A' and resid 1148 through 1155 removed outlier: 3.671A pdb=" N ASN A1155 " --> pdb=" O PHE A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1176 Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1197 through 1203 Processing helix chain 'A' and resid 1213 through 1217 Processing helix chain 'A' and resid 1220 through 1235 removed outlier: 4.067A pdb=" N ARG A1235 " --> pdb=" O ARG A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1265 removed outlier: 3.649A pdb=" N THR A1256 " --> pdb=" O GLU A1252 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A1263 " --> pdb=" O VAL A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1280 removed outlier: 3.778A pdb=" N ILE A1280 " --> pdb=" O LEU A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1308 through 1317 removed outlier: 3.640A pdb=" N GLY A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 445 removed outlier: 6.764A pdb=" N ILE A 437 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N HIS A 428 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A 439 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR A 426 " --> pdb=" O ASN A 439 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU A 441 " --> pdb=" O ASN A 424 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A 443 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE A 422 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR A 480 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASN A 424 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N MET A 478 " --> pdb=" O ASN A 424 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 498 through 501 removed outlier: 6.266A pdb=" N THR A 451 " --> pdb=" O SER A 612 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N MET A 450 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A 627 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA A 452 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE A 629 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 454 " --> pdb=" O PHE A 629 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1096 through 1097 removed outlier: 3.561A pdb=" N LEU A1096 " --> pdb=" O PHE A1085 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1096 through 1097 removed outlier: 3.561A pdb=" N LEU A1096 " --> pdb=" O PHE A1085 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A1136 " --> pdb=" O VAL A1081 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS A1083 " --> pdb=" O GLN A1134 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLN A1134 " --> pdb=" O CYS A1083 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1159 removed outlier: 6.266A pdb=" N GLY A1157 " --> pdb=" O LEU A1241 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ASP A1243 " --> pdb=" O GLY A1157 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A1159 " --> pdb=" O ASP A1243 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A1109 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR A1108 " --> pdb=" O ILE A1285 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA A1287 " --> pdb=" O THR A1108 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA A1110 " --> pdb=" O ALA A1287 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET A1289 " --> pdb=" O ALA A1110 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL A1112 " --> pdb=" O MET A1289 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU A1296 " --> pdb=" O VAL A1288 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA A1290 " --> pdb=" O VAL A1294 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL A1294 " --> pdb=" O ALA A1290 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1698 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: 3.69 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2890 1.35 - 1.49: 2275 1.49 - 1.62: 3909 1.62 - 1.76: 0 1.76 - 1.90: 89 Bond restraints: 9163 Sorted by residual: bond pdb=" C4 ADP A1506 " pdb=" C5 ADP A1506 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C5 ADP A1506 " pdb=" C6 ADP A1506 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O3B ADP A1506 " pdb=" PB ADP A1506 " ideal model delta sigma weight residual 1.510 1.463 0.047 2.00e-02 2.50e+03 5.63e+00 bond pdb=" C8 ADP A1506 " pdb=" N7 ADP A1506 " ideal model delta sigma weight residual 1.350 1.306 0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" N LYS A 829 " pdb=" CA LYS A 829 " ideal model delta sigma weight residual 1.458 1.486 -0.027 1.26e-02 6.30e+03 4.72e+00 ... (remaining 9158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 12343 3.20 - 6.40: 63 6.40 - 9.60: 12 9.60 - 12.79: 0 12.79 - 15.99: 1 Bond angle restraints: 12419 Sorted by residual: angle pdb=" PA ADP A1506 " pdb=" O3A ADP A1506 " pdb=" PB ADP A1506 " ideal model delta sigma weight residual 120.50 136.49 -15.99 3.00e+00 1.11e-01 2.84e+01 angle pdb=" C TYR A1037 " pdb=" N THR A1038 " pdb=" CA THR A1038 " ideal model delta sigma weight residual 120.09 125.08 -4.99 1.25e+00 6.40e-01 1.60e+01 angle pdb=" CA MET A 86 " pdb=" C MET A 86 " pdb=" O MET A 86 " ideal model delta sigma weight residual 120.55 116.61 3.94 1.06e+00 8.90e-01 1.38e+01 angle pdb=" O ALA A 739 " pdb=" C ALA A 739 " pdb=" N PRO A 740 " ideal model delta sigma weight residual 121.37 118.13 3.24 9.00e-01 1.23e+00 1.29e+01 angle pdb=" C LYS A 829 " pdb=" N ARG A 830 " pdb=" CA ARG A 830 " ideal model delta sigma weight residual 120.28 115.75 4.53 1.34e+00 5.57e-01 1.14e+01 ... (remaining 12414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 4967 17.41 - 34.81: 492 34.81 - 52.22: 148 52.22 - 69.63: 31 69.63 - 87.04: 9 Dihedral angle restraints: 5647 sinusoidal: 2401 harmonic: 3246 Sorted by residual: dihedral pdb=" O1B ADP A1506 " pdb=" O3A ADP A1506 " pdb=" PB ADP A1506 " pdb=" PA ADP A1506 " ideal model delta sinusoidal sigma weight residual -60.00 27.03 -87.04 1 2.00e+01 2.50e-03 2.28e+01 dihedral pdb=" CA MET A 138 " pdb=" C MET A 138 " pdb=" N ILE A 139 " pdb=" CA ILE A 139 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CG ARG A1050 " pdb=" CD ARG A1050 " pdb=" NE ARG A1050 " pdb=" CZ ARG A1050 " ideal model delta sinusoidal sigma weight residual 90.00 41.05 48.95 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 5644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 1417 0.177 - 0.354: 1 0.354 - 0.531: 0 0.531 - 0.708: 0 0.708 - 0.886: 1 Chirality restraints: 1419 Sorted by residual: chirality pdb=" V VO4 A1507 " pdb=" O1 VO4 A1507 " pdb=" O2 VO4 A1507 " pdb=" O4 VO4 A1507 " both_signs ideal model delta sigma weight residual True 5.36 4.48 0.89 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" C3' ADP A1506 " pdb=" C2' ADP A1506 " pdb=" C4' ADP A1506 " pdb=" O3' ADP A1506 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA MET A 138 " pdb=" N MET A 138 " pdb=" C MET A 138 " pdb=" CB MET A 138 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 1416 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 828 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C THR A 828 " 0.036 2.00e-02 2.50e+03 pdb=" O THR A 828 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 829 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 534 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" CD GLU A 534 " -0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU A 534 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 534 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 776 " 0.011 2.00e-02 2.50e+03 1.24e-02 2.70e+00 pdb=" CG PHE A 776 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 776 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 776 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 776 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 776 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 776 " 0.000 2.00e-02 2.50e+03 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 53 2.55 - 3.13: 6979 3.13 - 3.72: 14013 3.72 - 4.31: 19897 4.31 - 4.90: 33159 Nonbonded interactions: 74101 Sorted by model distance: nonbonded pdb="MG MG A1508 " pdb=" O HOH A1602 " model vdw 1.958 2.170 nonbonded pdb=" O3G ATP A1501 " pdb="MG MG A1509 " model vdw 1.958 2.170 nonbonded pdb="MG MG A1509 " pdb=" O HOH A1601 " model vdw 1.986 2.170 nonbonded pdb=" OG SER A 462 " pdb="MG MG A1509 " model vdw 1.995 2.170 nonbonded pdb=" OE1 GLN A1161 " pdb="MG MG A1508 " model vdw 2.017 2.170 ... (remaining 74096 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=0.00 max=1.00 mean=0.91 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: 4.930 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: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.790 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:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 0.112 9163 Z= 0.236 Angle : 0.640 15.993 12419 Z= 0.336 Chirality : 0.047 0.886 1419 Planarity : 0.003 0.039 1551 Dihedral : 15.655 87.036 3561 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1123 helix: 1.02 (0.19), residues: 748 sheet: 0.40 (0.60), residues: 76 loop : -1.18 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1071 HIS 0.004 0.001 HIS A 615 PHE 0.029 0.001 PHE A 776 TYR 0.025 0.001 TYR A 337 ARG 0.012 0.000 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 594 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8219 (tm-30) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 1.5306 time to fit residues: 190.0822 Evaluate side-chains 94 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 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 307 ASN A 312 GLN A 530 GLN A 885 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9163 Z= 0.207 Angle : 0.563 8.649 12419 Z= 0.295 Chirality : 0.042 0.161 1419 Planarity : 0.004 0.039 1551 Dihedral : 7.300 71.244 1525 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.99 % Allowed : 13.89 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1123 helix: 1.47 (0.19), residues: 759 sheet: 0.06 (0.56), residues: 74 loop : -1.36 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 314 HIS 0.002 0.001 HIS A 428 PHE 0.027 0.001 PHE A 776 TYR 0.020 0.001 TYR A 337 ARG 0.008 0.001 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8743 (mt) cc_final: 0.8492 (mt) REVERT: A 476 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8276 (tp30) REVERT: A 526 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7607 (tp30) REVERT: A 957 ARG cc_start: 0.7720 (mpp80) cc_final: 0.7511 (mtt90) REVERT: A 1252 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7333 (tp30) outliers start: 28 outliers final: 14 residues processed: 127 average time/residue: 1.3721 time to fit residues: 186.5055 Evaluate side-chains 112 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1252 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 85 optimal weight: 0.0870 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 530 GLN A 778 GLN A 885 ASN A 946 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9163 Z= 0.166 Angle : 0.499 7.024 12419 Z= 0.263 Chirality : 0.040 0.145 1419 Planarity : 0.003 0.043 1551 Dihedral : 6.757 80.393 1525 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.10 % Allowed : 15.06 % Favored : 81.84 % 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: 1.37 (0.25), residues: 1123 helix: 1.82 (0.19), residues: 758 sheet: 0.13 (0.56), residues: 74 loop : -1.32 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 163 HIS 0.002 0.001 HIS A 428 PHE 0.023 0.001 PHE A 776 TYR 0.020 0.001 TYR A 337 ARG 0.009 0.000 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7597 (t0) cc_final: 0.7332 (t0) REVERT: A 443 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8579 (ptt) REVERT: A 476 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8296 (tp30) REVERT: A 526 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7549 (tp30) REVERT: A 530 GLN cc_start: 0.7933 (tp40) cc_final: 0.6614 (tp-100) REVERT: A 534 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: A 778 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7274 (mm-40) REVERT: A 957 ARG cc_start: 0.7676 (mpp80) cc_final: 0.7459 (mtt90) REVERT: A 989 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.6627 (mm-40) REVERT: A 1180 THR cc_start: 0.7296 (p) cc_final: 0.7069 (p) outliers start: 29 outliers final: 14 residues processed: 128 average time/residue: 1.5648 time to fit residues: 211.8127 Evaluate side-chains 117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 778 GLN Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 312 GLN A 885 ASN A 941 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9163 Z= 0.162 Angle : 0.495 7.185 12419 Z= 0.259 Chirality : 0.040 0.149 1419 Planarity : 0.003 0.034 1551 Dihedral : 6.636 82.485 1525 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.78 % Allowed : 16.35 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.25), residues: 1123 helix: 1.91 (0.19), residues: 758 sheet: 0.27 (0.55), residues: 74 loop : -1.29 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1071 HIS 0.003 0.001 HIS A 615 PHE 0.024 0.001 PHE A 776 TYR 0.014 0.001 TYR A 337 ARG 0.008 0.000 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7603 (t0) cc_final: 0.7333 (t0) REVERT: A 243 LEU cc_start: 0.4829 (OUTLIER) cc_final: 0.4552 (pp) REVERT: A 476 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8292 (tp30) REVERT: A 526 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7529 (tp30) REVERT: A 554 GLU cc_start: 0.7571 (tp30) cc_final: 0.7281 (tp30) REVERT: A 957 ARG cc_start: 0.7692 (mpp80) cc_final: 0.7489 (mtt90) REVERT: A 989 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.6613 (mm-40) REVERT: A 1180 THR cc_start: 0.7335 (p) cc_final: 0.7110 (p) REVERT: A 1186 GLU cc_start: 0.7728 (tp30) cc_final: 0.7494 (mp0) outliers start: 26 outliers final: 16 residues processed: 118 average time/residue: 1.4494 time to fit residues: 181.6138 Evaluate side-chains 113 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 98 optimal weight: 0.0870 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 530 GLN A 778 GLN A 885 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9163 Z= 0.233 Angle : 0.549 7.864 12419 Z= 0.288 Chirality : 0.042 0.176 1419 Planarity : 0.004 0.041 1551 Dihedral : 6.877 80.189 1525 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.85 % Allowed : 14.64 % Favored : 81.52 % 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: 1.26 (0.24), residues: 1123 helix: 1.68 (0.18), residues: 761 sheet: 0.14 (0.54), residues: 74 loop : -1.27 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 846 HIS 0.003 0.001 HIS A 428 PHE 0.022 0.001 PHE A 776 TYR 0.016 0.002 TYR A 337 ARG 0.011 0.001 ARG A 299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7594 (t0) cc_final: 0.7324 (t0) REVERT: A 243 LEU cc_start: 0.4727 (OUTLIER) cc_final: 0.4477 (pp) REVERT: A 476 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8278 (tp30) REVERT: A 526 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7543 (tp30) REVERT: A 554 GLU cc_start: 0.7615 (tp30) cc_final: 0.7308 (tp30) REVERT: A 594 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 957 ARG cc_start: 0.7759 (mpp80) cc_final: 0.7467 (mtt90) REVERT: A 989 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.6786 (mm-40) REVERT: A 1186 GLU cc_start: 0.7815 (tp30) cc_final: 0.7563 (mp0) outliers start: 36 outliers final: 22 residues processed: 127 average time/residue: 1.4393 time to fit residues: 195.6980 Evaluate side-chains 118 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.0010 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN A 312 GLN A 530 GLN A 885 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9163 Z= 0.161 Angle : 0.494 6.657 12419 Z= 0.259 Chirality : 0.040 0.162 1419 Planarity : 0.003 0.038 1551 Dihedral : 6.468 84.552 1525 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.63 % Allowed : 15.49 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.57 (0.25), residues: 1123 helix: 1.93 (0.19), residues: 761 sheet: 0.32 (0.55), residues: 74 loop : -1.21 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1071 HIS 0.002 0.001 HIS A 428 PHE 0.024 0.001 PHE A 776 TYR 0.016 0.001 TYR A 337 ARG 0.010 0.000 ARG A 299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7591 (t0) cc_final: 0.7327 (t0) REVERT: A 243 LEU cc_start: 0.4655 (OUTLIER) cc_final: 0.4397 (pp) REVERT: A 476 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8286 (tp30) REVERT: A 526 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7486 (tp30) REVERT: A 554 GLU cc_start: 0.7575 (tp30) cc_final: 0.7282 (tp30) REVERT: A 957 ARG cc_start: 0.7740 (mpp80) cc_final: 0.7420 (mtt90) REVERT: A 989 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.6644 (mm-40) REVERT: A 1180 THR cc_start: 0.7346 (p) cc_final: 0.7115 (p) REVERT: A 1186 GLU cc_start: 0.7788 (tp30) cc_final: 0.7542 (mp0) outliers start: 34 outliers final: 22 residues processed: 126 average time/residue: 1.3984 time to fit residues: 187.6347 Evaluate side-chains 116 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 0.0670 chunk 68 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 530 GLN A 885 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9163 Z= 0.243 Angle : 0.558 7.567 12419 Z= 0.293 Chirality : 0.042 0.145 1419 Planarity : 0.004 0.039 1551 Dihedral : 6.781 80.870 1525 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.06 % Allowed : 15.60 % Favored : 80.34 % 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: 1.33 (0.25), residues: 1123 helix: 1.73 (0.18), residues: 763 sheet: 0.08 (0.54), residues: 74 loop : -1.20 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 846 HIS 0.003 0.001 HIS A 428 PHE 0.024 0.002 PHE A 776 TYR 0.017 0.001 TYR A 337 ARG 0.009 0.001 ARG A 299 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7603 (t0) cc_final: 0.7323 (t0) REVERT: A 243 LEU cc_start: 0.4580 (OUTLIER) cc_final: 0.4359 (pp) REVERT: A 476 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8288 (tp30) REVERT: A 521 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7482 (mm-30) REVERT: A 526 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7541 (tp30) REVERT: A 554 GLU cc_start: 0.7629 (tp30) cc_final: 0.7341 (tp30) REVERT: A 957 ARG cc_start: 0.7792 (mpp80) cc_final: 0.7468 (mtt90) REVERT: A 989 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.6779 (mm-40) REVERT: A 1180 THR cc_start: 0.7414 (p) cc_final: 0.7117 (p) REVERT: A 1186 GLU cc_start: 0.7801 (tp30) cc_final: 0.7542 (mp0) outliers start: 38 outliers final: 23 residues processed: 121 average time/residue: 1.3769 time to fit residues: 177.4181 Evaluate side-chains 113 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 361 GLN A 530 GLN A 885 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9163 Z= 0.360 Angle : 0.647 8.666 12419 Z= 0.338 Chirality : 0.046 0.200 1419 Planarity : 0.004 0.046 1551 Dihedral : 7.328 75.503 1525 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.17 % Allowed : 16.13 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.24), residues: 1123 helix: 1.32 (0.18), residues: 761 sheet: -0.20 (0.54), residues: 69 loop : -1.29 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 846 HIS 0.004 0.001 HIS A 428 PHE 0.024 0.002 PHE A 776 TYR 0.016 0.002 TYR A 337 ARG 0.011 0.001 ARG A 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7625 (t0) cc_final: 0.7376 (t0) REVERT: A 172 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7776 (tp40) REVERT: A 411 TYR cc_start: 0.7440 (t80) cc_final: 0.7184 (t80) REVERT: A 476 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8310 (tp30) REVERT: A 526 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: A 989 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.6944 (mm-40) REVERT: A 1186 GLU cc_start: 0.7820 (tp30) cc_final: 0.7560 (mp0) outliers start: 39 outliers final: 24 residues processed: 124 average time/residue: 1.4005 time to fit residues: 184.7946 Evaluate side-chains 120 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1295 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 530 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9163 Z= 0.183 Angle : 0.540 7.343 12419 Z= 0.283 Chirality : 0.041 0.173 1419 Planarity : 0.003 0.042 1551 Dihedral : 6.775 82.577 1525 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.99 % Allowed : 17.09 % Favored : 79.91 % 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: 1.27 (0.25), residues: 1123 helix: 1.72 (0.19), residues: 761 sheet: -0.11 (0.52), residues: 74 loop : -1.27 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 493 HIS 0.002 0.001 HIS A 615 PHE 0.023 0.001 PHE A 776 TYR 0.016 0.001 TYR A 337 ARG 0.010 0.000 ARG A 299 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7607 (t0) cc_final: 0.7356 (t0) REVERT: A 476 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8328 (tp30) REVERT: A 526 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7510 (tp30) REVERT: A 957 ARG cc_start: 0.7804 (mpp80) cc_final: 0.7474 (mtt90) REVERT: A 989 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.6745 (mm-40) REVERT: A 1180 THR cc_start: 0.7390 (p) cc_final: 0.7154 (p) REVERT: A 1186 GLU cc_start: 0.7816 (tp30) cc_final: 0.7537 (mp0) outliers start: 28 outliers final: 22 residues processed: 111 average time/residue: 1.5105 time to fit residues: 178.3051 Evaluate side-chains 110 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 chunk 95 optimal weight: 0.4980 chunk 27 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 492 GLN A 530 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9163 Z= 0.153 Angle : 0.518 6.678 12419 Z= 0.270 Chirality : 0.040 0.167 1419 Planarity : 0.003 0.042 1551 Dihedral : 6.293 85.834 1525 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.46 % Allowed : 17.84 % Favored : 79.70 % 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: 1.64 (0.25), residues: 1123 helix: 2.00 (0.19), residues: 762 sheet: 0.11 (0.53), residues: 74 loop : -1.19 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 493 HIS 0.002 0.001 HIS A 615 PHE 0.022 0.001 PHE A 776 TYR 0.016 0.001 TYR A 337 ARG 0.011 0.000 ARG A1050 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.013 Fit side-chains REVERT: A 94 ASP cc_start: 0.7571 (t0) cc_final: 0.7305 (t0) REVERT: A 476 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: A 526 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7459 (tp30) REVERT: A 957 ARG cc_start: 0.7776 (mpp80) cc_final: 0.7444 (mtt90) REVERT: A 989 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.6563 (mm-40) REVERT: A 1172 ASP cc_start: 0.8510 (m-30) cc_final: 0.8309 (m-30) REVERT: A 1180 THR cc_start: 0.7333 (p) cc_final: 0.7106 (p) REVERT: A 1186 GLU cc_start: 0.7850 (tp30) cc_final: 0.7579 (mp0) outliers start: 23 outliers final: 15 residues processed: 112 average time/residue: 1.3988 time to fit residues: 167.4718 Evaluate side-chains 105 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 530 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103973 restraints weight = 12858.680| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.26 r_work: 0.3140 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 161 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 257 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9163 Z= 0.188 Angle : 0.547 10.037 12419 Z= 0.286 Chirality : 0.040 0.142 1419 Planarity : 0.003 0.042 1551 Dihedral : 6.365 83.410 1525 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.35 % Allowed : 18.48 % Favored : 79.17 % 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: 1.60 (0.25), residues: 1123 helix: 1.96 (0.19), residues: 764 sheet: 0.12 (0.53), residues: 74 loop : -1.18 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 314 HIS 0.002 0.001 HIS A 428 PHE 0.023 0.001 PHE A 776 TYR 0.016 0.001 TYR A 337 ARG 0.010 0.000 ARG A1050 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3845.50 seconds wall clock time: 69 minutes 44.03 seconds (4184.03 seconds total)