Starting phenix.real_space_refine on Thu Jul 2 19:05:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bwp_16293/07_2026/8bwp_16293.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bwp_16293/07_2026/8bwp_16293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bwp_16293/07_2026/8bwp_16293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bwp_16293/07_2026/8bwp_16293.map" model { file = "/net/cci-nas-00/data/ceres_data/8bwp_16293/07_2026/8bwp_16293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bwp_16293/07_2026/8bwp_16293.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8bwp_16293/07_2026/8bwp_16293.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bwp_16293/07_2026/8bwp_16293.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.070 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 43 5.16 5 C 6221 2.51 5 N 1610 2.21 5 O 1704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9578 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9545 Classifications: {'peptide': 1195} Link IDs: {'PTRANS': 37, 'TRANS': 1157} Chain breaks: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'MTX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.74, per 1000 atoms: 0.18 Number of scatterers: 9578 At special positions: 0 Unit cell: (77.376, 107.328, 144.768, 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 43 16.00 O 1704 8.00 N 1610 7.00 C 6221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 318.7 milliseconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB MTX A1401 " Number of C-beta restraints generated: 2266 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 5 sheets defined 73.1% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.742A pdb=" N PHE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 75 removed outlier: 4.316A pdb=" N GLY A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.769A pdb=" N ALA A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 121 removed outlier: 4.157A pdb=" N LEU A 93 " --> pdb=" O TRP A 89 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.578A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 150 Processing helix chain 'A' and resid 150 through 181 removed outlier: 3.956A pdb=" N LEU A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.337A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 235 through 246 removed outlier: 3.944A pdb=" N ALA A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 282 removed outlier: 3.893A pdb=" N LEU A 250 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 291 through 342 removed outlier: 4.369A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 367 removed outlier: 3.690A pdb=" N ALA A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.509A pdb=" N LEU A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 513 through 521 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.534A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 576 removed outlier: 4.392A pdb=" N PHE A 574 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 removed outlier: 3.873A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 697 through 709 removed outlier: 3.505A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 745 removed outlier: 3.647A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 808 removed outlier: 3.708A pdb=" N GLY A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 803 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.697A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 removed outlier: 3.636A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 removed outlier: 4.611A pdb=" N ASP A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 861 Processing helix chain 'A' and resid 864 through 896 Proline residue: A 870 - end of helix removed outlier: 3.599A pdb=" N ARG A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.891A pdb=" N PHE A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.724A pdb=" N TYR A 917 " --> pdb=" O THR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 970 removed outlier: 4.016A pdb=" N CYS A 923 " --> pdb=" O ALA A 919 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 927 " --> pdb=" O CYS A 923 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU A 936 " --> pdb=" O ASP A 932 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 945 " --> pdb=" O PHE A 941 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 987 Processing helix chain 'A' and resid 988 through 1007 removed outlier: 3.524A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP A 995 " --> pdb=" O GLY A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1018 removed outlier: 3.772A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1089 Processing helix chain 'A' and resid 1109 through 1116 removed outlier: 3.689A pdb=" N LYS A1115 " --> pdb=" O HIS A1111 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A1116 " --> pdb=" O ASP A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1155 through 1161 Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1171 through 1175 Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1203 through 1207 Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1234 through 1238 Processing helix chain 'A' and resid 1257 through 1264 Processing helix chain 'A' and resid 1267 through 1275 Processing helix chain 'A' and resid 1276 through 1278 No H-bonds generated for 'chain 'A' and resid 1276 through 1278' Processing helix chain 'A' and resid 1279 through 1294 Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435 removed outlier: 5.804A pdb=" N GLN A 429 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA A 417 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE A 433 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLN A 413 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 435 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N HIS A 411 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A 415 " --> pdb=" O HIS A 466 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS A 466 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.847A pdb=" N ALA A 476 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA A 442 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU A 606 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 444 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 removed outlier: 4.644A pdb=" N GLY A 487 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1058 through 1065 removed outlier: 5.790A pdb=" N LYS A1059 " --> pdb=" O PHE A1048 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE A1048 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ALA A1063 " --> pdb=" O ASP A1044 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP A1044 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE A1065 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE A1042 " --> pdb=" O ILE A1065 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A1046 " --> pdb=" O GLU A1095 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU A1095 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1117 through 1120 removed outlier: 6.451A pdb=" N LEU A1198 " --> pdb=" O LEU A1229 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE A1231 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A1200 " --> pdb=" O ILE A1231 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS A1070 " --> pdb=" O LYS A1243 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N MET A1245 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1761 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3024 1.34 - 1.46: 1607 1.46 - 1.58: 5082 1.58 - 1.69: 1 1.69 - 1.81: 70 Bond restraints: 9784 Sorted by residual: bond pdb=" C2 MTX A1401 " pdb=" NA2 MTX A1401 " ideal model delta sigma weight residual 1.341 1.407 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" CG LEU A 27 " pdb=" CD1 LEU A 27 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.97e+00 bond pdb=" CB GLN A 931 " pdb=" CG GLN A 931 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.12e+00 bond pdb=" C8A MTX A1401 " pdb=" N8 MTX A1401 " ideal model delta sigma weight residual 1.348 1.393 -0.045 2.00e-02 2.50e+03 5.09e+00 bond pdb=" CB ARG A 946 " pdb=" CG ARG A 946 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.09e+00 ... (remaining 9779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 12676 1.88 - 3.77: 488 3.77 - 5.65: 75 5.65 - 7.54: 18 7.54 - 9.42: 5 Bond angle restraints: 13262 Sorted by residual: angle pdb=" C THR A 943 " pdb=" N THR A 944 " pdb=" CA THR A 944 " ideal model delta sigma weight residual 120.29 115.76 4.53 1.42e+00 4.96e-01 1.02e+01 angle pdb=" CB ARG A 951 " pdb=" CG ARG A 951 " pdb=" CD ARG A 951 " ideal model delta sigma weight residual 111.30 118.25 -6.95 2.30e+00 1.89e-01 9.12e+00 angle pdb=" CA GLN A 849 " pdb=" CB GLN A 849 " pdb=" CG GLN A 849 " ideal model delta sigma weight residual 114.10 120.10 -6.00 2.00e+00 2.50e-01 9.00e+00 angle pdb=" C HIS A 153 " pdb=" N LEU A 154 " pdb=" CA LEU A 154 " ideal model delta sigma weight residual 120.29 116.07 4.22 1.42e+00 4.96e-01 8.84e+00 angle pdb=" CA ARG A 951 " pdb=" CB ARG A 951 " pdb=" CG ARG A 951 " ideal model delta sigma weight residual 114.10 119.50 -5.40 2.00e+00 2.50e-01 7.30e+00 ... (remaining 13257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 5411 16.96 - 33.92: 324 33.92 - 50.87: 70 50.87 - 67.83: 17 67.83 - 84.79: 5 Dihedral angle restraints: 5827 sinusoidal: 2333 harmonic: 3494 Sorted by residual: dihedral pdb=" CA LEU A1091 " pdb=" C LEU A1091 " pdb=" N SER A1092 " pdb=" CA SER A1092 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA CYS A1226 " pdb=" C CYS A1226 " pdb=" N THR A1227 " pdb=" CA THR A1227 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA LYS A1021 " pdb=" C LYS A1021 " pdb=" N GLU A1022 " pdb=" CA GLU A1022 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 5824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1187 0.068 - 0.136: 309 0.136 - 0.204: 38 0.204 - 0.272: 3 0.272 - 0.340: 1 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CA MTX A1401 " pdb=" N MTX A1401 " pdb=" CB MTX A1401 " pdb=" CT MTX A1401 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA PHE A 258 " pdb=" N PHE A 258 " pdb=" C PHE A 258 " pdb=" CB PHE A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA PHE A 24 " pdb=" N PHE A 24 " pdb=" C PHE A 24 " pdb=" CB PHE A 24 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1535 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 26 " -0.020 2.00e-02 2.50e+03 1.55e-02 5.98e+00 pdb=" CG TRP A 26 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 26 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 26 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 26 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 26 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 26 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 26 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 26 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 26 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 939 " -0.024 2.00e-02 2.50e+03 1.84e-02 5.91e+00 pdb=" CG PHE A 939 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 939 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 939 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 939 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 939 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 939 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1292 " 0.009 2.00e-02 2.50e+03 1.64e-02 5.40e+00 pdb=" CG TYR A1292 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A1292 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A1292 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A1292 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR A1292 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1292 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR A1292 " 0.027 2.00e-02 2.50e+03 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1421 2.75 - 3.29: 10324 3.29 - 3.83: 15536 3.83 - 4.36: 18837 4.36 - 4.90: 31944 Nonbonded interactions: 78062 Sorted by model distance: nonbonded pdb=" NH1 ARG A 303 " pdb=" OE1 GLU A 306 " model vdw 2.213 3.120 nonbonded pdb=" OH TYR A 92 " pdb=" O THR A 209 " model vdw 2.214 3.040 nonbonded pdb=" O SER A1241 " pdb=" OH TYR A1292 " model vdw 2.219 3.040 nonbonded pdb=" O GLU A 521 " pdb=" OG1 THR A 526 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR A 269 " pdb=" OE2 GLU A 306 " model vdw 2.247 3.040 ... (remaining 78057 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.011 0.081 9784 Z= 0.457 Angle : 0.899 9.422 13262 Z= 0.492 Chirality : 0.060 0.340 1538 Planarity : 0.008 0.078 1646 Dihedral : 12.352 84.791 3561 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.48 % Allowed : 1.82 % Favored : 97.70 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.22), residues: 1187 helix: -1.44 (0.15), residues: 769 sheet: 0.56 (0.78), residues: 50 loop : 0.32 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG A 897 TYR 0.028 0.005 TYR A 881 PHE 0.042 0.004 PHE A 939 TRP 0.042 0.003 TRP A 26 HIS 0.014 0.002 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.01091 / 0.46 ( 9784) covalent geometry : angle 0.89889 / 0.49 (13262) hydrogen bonds : bond 0.22442 / 15.16 ( 609) hydrogen bonds : angle 8.61477 / 6.13 ( 1761) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 207 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8467 (t0) cc_final: 0.8211 (t0) REVERT: A 67 GLU cc_start: 0.8510 (tp30) cc_final: 0.8278 (tp30) REVERT: A 200 ASN cc_start: 0.8411 (t0) cc_final: 0.7787 (t0) REVERT: A 206 ASP cc_start: 0.7918 (t70) cc_final: 0.7708 (t70) REVERT: A 276 MET cc_start: 0.8329 (tpp) cc_final: 0.8109 (tpp) REVERT: A 316 LEU cc_start: 0.8398 (tp) cc_final: 0.7992 (tt) REVERT: A 728 TYR cc_start: 0.8546 (t80) cc_final: 0.8310 (t80) REVERT: A 953 ASP cc_start: 0.8493 (m-30) cc_final: 0.7945 (m-30) REVERT: A 985 TYR cc_start: 0.8166 (m-80) cc_final: 0.7717 (m-80) REVERT: A 998 ARG cc_start: 0.7298 (ttm-80) cc_final: 0.7020 (mmt-90) REVERT: A 1045 ASN cc_start: 0.9065 (t0) cc_final: 0.8806 (t0) REVERT: A 1104 LEU cc_start: 0.9073 (tp) cc_final: 0.8539 (tp) REVERT: A 1122 GLN cc_start: 0.7517 (tt0) cc_final: 0.6847 (tm-30) REVERT: A 1136 ASP cc_start: 0.7587 (t0) cc_final: 0.6875 (t0) REVERT: A 1196 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7621 (mp10) REVERT: A 1212 ASP cc_start: 0.8769 (t0) cc_final: 0.8278 (m-30) REVERT: A 1253 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8766 (mmtm) outliers start: 5 outliers final: 3 residues processed: 211 average time/residue: 0.0992 time to fit residues: 28.0335 Evaluate side-chains 140 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1216 GLN ** 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 = 0.4227 r_free = 0.4227 target = 0.199316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.157876 restraints weight = 11634.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155577 restraints weight = 12947.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.156985 restraints weight = 12786.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.158173 restraints weight = 7169.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.161644 restraints weight = 5793.267| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9784 Z= 0.161 Angle : 0.608 8.170 13262 Z= 0.329 Chirality : 0.043 0.181 1538 Planarity : 0.004 0.037 1646 Dihedral : 5.407 31.247 1296 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.82 % Allowed : 8.06 % Favored : 90.12 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1187 helix: 0.29 (0.18), residues: 789 sheet: 0.53 (0.76), residues: 52 loop : 0.54 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1220 TYR 0.024 0.002 TYR A1292 PHE 0.034 0.002 PHE A 258 TRP 0.013 0.001 TRP A 711 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 9784) covalent geometry : angle 0.60830 / 0.33 (13262) hydrogen bonds : bond 0.05160 / 3.47 ( 609) hydrogen bonds : angle 4.94922 / 3.56 ( 1761) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ASN cc_start: 0.8347 (t0) cc_final: 0.8106 (t0) REVERT: A 706 ARG cc_start: 0.7887 (tpp-160) cc_final: 0.7534 (mmt180) REVERT: A 744 MET cc_start: 0.7368 (mmm) cc_final: 0.6878 (mtp) REVERT: A 990 MET cc_start: 0.7673 (pmm) cc_final: 0.7404 (ptp) REVERT: A 1016 TYR cc_start: 0.7746 (m-10) cc_final: 0.6650 (m-10) REVERT: A 1136 ASP cc_start: 0.7839 (t0) cc_final: 0.7230 (t70) outliers start: 19 outliers final: 14 residues processed: 199 average time/residue: 0.0785 time to fit residues: 22.2525 Evaluate side-chains 154 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1064 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 113 optimal weight: 0.1980 chunk 45 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1134 ASN A1206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.197244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.155696 restraints weight = 11638.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152905 restraints weight = 15955.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.155207 restraints weight = 14280.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.155656 restraints weight = 7975.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156626 restraints weight = 6903.047| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9784 Z= 0.208 Angle : 0.623 9.740 13262 Z= 0.328 Chirality : 0.044 0.189 1538 Planarity : 0.004 0.035 1646 Dihedral : 5.067 24.874 1294 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.84 % Allowed : 10.56 % Favored : 85.60 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.25), residues: 1187 helix: 0.48 (0.18), residues: 786 sheet: 1.08 (0.81), residues: 47 loop : 0.61 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1030 TYR 0.021 0.002 TYR A 289 PHE 0.033 0.002 PHE A 258 TRP 0.014 0.002 TRP A 26 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 ( 9784) covalent geometry : angle 0.62256 / 0.33 (13262) hydrogen bonds : bond 0.04967 / 3.34 ( 609) hydrogen bonds : angle 4.81560 / 3.47 ( 1761) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8668 (tp40) cc_final: 0.8354 (tp40) REVERT: A 67 GLU cc_start: 0.8721 (tp30) cc_final: 0.8358 (tp30) REVERT: A 706 ARG cc_start: 0.7927 (tpp-160) cc_final: 0.7511 (mmt180) REVERT: A 744 MET cc_start: 0.7382 (mmm) cc_final: 0.7043 (mtt) REVERT: A 904 LEU cc_start: 0.8436 (tp) cc_final: 0.8217 (tp) REVERT: A 1016 TYR cc_start: 0.7681 (m-10) cc_final: 0.6699 (m-10) REVERT: A 1122 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7703 (tp40) REVERT: A 1136 ASP cc_start: 0.7975 (t0) cc_final: 0.7373 (t0) outliers start: 40 outliers final: 30 residues processed: 178 average time/residue: 0.0744 time to fit residues: 19.3131 Evaluate side-chains 163 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 0.0770 chunk 45 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1068 GLN A1134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.201608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.161682 restraints weight = 11468.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158645 restraints weight = 13362.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.160560 restraints weight = 13356.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.161662 restraints weight = 7076.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.162299 restraints weight = 5904.439| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9784 Z= 0.141 Angle : 0.556 6.836 13262 Z= 0.294 Chirality : 0.041 0.170 1538 Planarity : 0.004 0.033 1646 Dihedral : 4.845 19.120 1294 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.59 % Allowed : 12.38 % Favored : 85.03 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.25), residues: 1187 helix: 0.75 (0.19), residues: 788 sheet: 1.17 (0.83), residues: 47 loop : 0.60 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1030 TYR 0.026 0.002 TYR A 289 PHE 0.033 0.002 PHE A 258 TRP 0.013 0.001 TRP A1025 HIS 0.004 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 9784) covalent geometry : angle 0.55572 / 0.29 (13262) hydrogen bonds : bond 0.04317 / 2.90 ( 609) hydrogen bonds : angle 4.51731 / 3.26 ( 1761) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8651 (tp40) cc_final: 0.8186 (tp-100) REVERT: A 241 MET cc_start: 0.7777 (mmm) cc_final: 0.7468 (mmm) REVERT: A 289 TYR cc_start: 0.7927 (m-80) cc_final: 0.7664 (m-80) REVERT: A 706 ARG cc_start: 0.7872 (tpp-160) cc_final: 0.7499 (mmt180) REVERT: A 728 TYR cc_start: 0.7944 (t80) cc_final: 0.7718 (t80) REVERT: A 744 MET cc_start: 0.7265 (mmm) cc_final: 0.6904 (mtt) REVERT: A 1016 TYR cc_start: 0.7662 (m-10) cc_final: 0.6758 (m-10) REVERT: A 1122 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7788 (tp40) REVERT: A 1132 ARG cc_start: 0.7508 (tpt-90) cc_final: 0.7197 (mmm-85) REVERT: A 1136 ASP cc_start: 0.7988 (t0) cc_final: 0.7420 (t0) outliers start: 27 outliers final: 22 residues processed: 166 average time/residue: 0.0782 time to fit residues: 18.4787 Evaluate side-chains 158 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1118 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 112 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1183 GLN ** 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 = 0.4234 r_free = 0.4234 target = 0.199655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.158811 restraints weight = 11515.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.158044 restraints weight = 13281.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.159231 restraints weight = 12316.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.159930 restraints weight = 6678.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.160554 restraints weight = 5623.716| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9784 Z= 0.171 Angle : 0.577 8.534 13262 Z= 0.302 Chirality : 0.042 0.176 1538 Planarity : 0.004 0.034 1646 Dihedral : 4.772 19.446 1294 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.88 % Allowed : 12.76 % Favored : 84.36 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.25), residues: 1187 helix: 0.78 (0.19), residues: 788 sheet: 1.22 (0.81), residues: 47 loop : 0.59 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1030 TYR 0.023 0.002 TYR A 289 PHE 0.033 0.002 PHE A 258 TRP 0.012 0.001 TRP A1099 HIS 0.004 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 9784) covalent geometry : angle 0.57671 / 0.30 (13262) hydrogen bonds : bond 0.04354 / 2.93 ( 609) hydrogen bonds : angle 4.50788 / 3.26 ( 1761) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8647 (tp40) cc_final: 0.8154 (tp-100) REVERT: A 276 MET cc_start: 0.7881 (mmm) cc_final: 0.7414 (mmm) REVERT: A 289 TYR cc_start: 0.8003 (m-80) cc_final: 0.7778 (m-80) REVERT: A 706 ARG cc_start: 0.7823 (tpp-160) cc_final: 0.7413 (mmt180) REVERT: A 744 MET cc_start: 0.7075 (mmm) cc_final: 0.6800 (mtt) REVERT: A 904 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8199 (tp) REVERT: A 1016 TYR cc_start: 0.7711 (m-10) cc_final: 0.6796 (m-10) REVERT: A 1120 ILE cc_start: 0.8926 (mp) cc_final: 0.8649 (pt) REVERT: A 1122 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7869 (tp40) REVERT: A 1132 ARG cc_start: 0.7483 (tpt-90) cc_final: 0.7160 (mmm-85) REVERT: A 1136 ASP cc_start: 0.7992 (t0) cc_final: 0.7564 (t0) outliers start: 30 outliers final: 27 residues processed: 164 average time/residue: 0.0852 time to fit residues: 20.1500 Evaluate side-chains 163 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 33 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 116 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.202043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.161109 restraints weight = 11510.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159908 restraints weight = 13018.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.161371 restraints weight = 12950.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.162046 restraints weight = 7355.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.162714 restraints weight = 6382.294| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9784 Z= 0.126 Angle : 0.549 9.561 13262 Z= 0.286 Chirality : 0.040 0.169 1538 Planarity : 0.003 0.035 1646 Dihedral : 4.602 18.568 1294 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.59 % Allowed : 13.53 % Favored : 83.88 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.25), residues: 1187 helix: 1.00 (0.19), residues: 789 sheet: 1.07 (0.80), residues: 47 loop : 0.64 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1030 TYR 0.021 0.001 TYR A 289 PHE 0.034 0.001 PHE A 258 TRP 0.015 0.001 TRP A1099 HIS 0.003 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 9784) covalent geometry : angle 0.54918 / 0.29 (13262) hydrogen bonds : bond 0.03982 / 2.67 ( 609) hydrogen bonds : angle 4.32017 / 3.13 ( 1761) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8580 (tp40) cc_final: 0.8070 (tp-100) REVERT: A 276 MET cc_start: 0.7715 (mmm) cc_final: 0.7472 (mmm) REVERT: A 289 TYR cc_start: 0.7904 (m-80) cc_final: 0.7696 (m-80) REVERT: A 367 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7688 (mt) REVERT: A 706 ARG cc_start: 0.7825 (tpp-160) cc_final: 0.7450 (mmt180) REVERT: A 744 MET cc_start: 0.7008 (mmm) cc_final: 0.6786 (mtt) REVERT: A 904 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8098 (tp) REVERT: A 1016 TYR cc_start: 0.7625 (m-10) cc_final: 0.6814 (m-10) REVERT: A 1122 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7921 (tp40) REVERT: A 1132 ARG cc_start: 0.7433 (tpt-90) cc_final: 0.7126 (mmm-85) REVERT: A 1136 ASP cc_start: 0.7995 (t0) cc_final: 0.7603 (t0) outliers start: 27 outliers final: 20 residues processed: 162 average time/residue: 0.0843 time to fit residues: 19.7231 Evaluate side-chains 156 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1169 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.199718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.158094 restraints weight = 11480.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.157988 restraints weight = 14322.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.159243 restraints weight = 12234.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.159822 restraints weight = 6964.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.161029 restraints weight = 5849.521| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9784 Z= 0.164 Angle : 0.561 8.125 13262 Z= 0.291 Chirality : 0.041 0.174 1538 Planarity : 0.004 0.036 1646 Dihedral : 4.565 19.127 1294 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.07 % Allowed : 14.30 % Favored : 82.63 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.25), residues: 1187 helix: 0.94 (0.19), residues: 791 sheet: 1.24 (0.80), residues: 47 loop : 0.68 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1030 TYR 0.021 0.002 TYR A 917 PHE 0.034 0.002 PHE A 258 TRP 0.011 0.001 TRP A1099 HIS 0.003 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 9784) covalent geometry : angle 0.56119 / 0.29 (13262) hydrogen bonds : bond 0.04116 / 2.77 ( 609) hydrogen bonds : angle 4.38337 / 3.18 ( 1761) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8638 (tp40) cc_final: 0.8105 (tp-100) REVERT: A 241 MET cc_start: 0.7682 (mmm) cc_final: 0.7470 (mmm) REVERT: A 276 MET cc_start: 0.7715 (mmm) cc_final: 0.7509 (mmm) REVERT: A 285 ILE cc_start: 0.8966 (tp) cc_final: 0.8697 (tp) REVERT: A 706 ARG cc_start: 0.7814 (tpp-160) cc_final: 0.7404 (mmt180) REVERT: A 744 MET cc_start: 0.7188 (mmm) cc_final: 0.6922 (mtt) REVERT: A 904 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8126 (tp) REVERT: A 1016 TYR cc_start: 0.7625 (m-10) cc_final: 0.6850 (m-10) REVERT: A 1120 ILE cc_start: 0.8871 (mp) cc_final: 0.8592 (pt) REVERT: A 1122 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7966 (tp40) REVERT: A 1136 ASP cc_start: 0.8044 (t0) cc_final: 0.7559 (t0) outliers start: 32 outliers final: 28 residues processed: 161 average time/residue: 0.0728 time to fit residues: 16.9132 Evaluate side-chains 160 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1169 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.200938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.159853 restraints weight = 11412.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.157264 restraints weight = 14242.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.159397 restraints weight = 13057.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.159980 restraints weight = 7367.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.160812 restraints weight = 6361.519| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9784 Z= 0.145 Angle : 0.562 8.307 13262 Z= 0.290 Chirality : 0.041 0.215 1538 Planarity : 0.003 0.036 1646 Dihedral : 4.505 18.691 1294 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.98 % Allowed : 14.88 % Favored : 82.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.25), residues: 1187 helix: 1.01 (0.19), residues: 791 sheet: 1.15 (0.70), residues: 58 loop : 0.70 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1030 TYR 0.030 0.002 TYR A 289 PHE 0.033 0.002 PHE A 258 TRP 0.012 0.001 TRP A1099 HIS 0.003 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 9784) covalent geometry : angle 0.56223 / 0.29 (13262) hydrogen bonds : bond 0.04009 / 2.69 ( 609) hydrogen bonds : angle 4.32418 / 3.14 ( 1761) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8638 (tp40) cc_final: 0.8087 (tp-100) REVERT: A 276 MET cc_start: 0.7577 (mmm) cc_final: 0.7360 (mmm) REVERT: A 706 ARG cc_start: 0.7795 (tpp-160) cc_final: 0.7403 (mmt180) REVERT: A 744 MET cc_start: 0.7355 (mmm) cc_final: 0.7038 (mtt) REVERT: A 1016 TYR cc_start: 0.7562 (m-10) cc_final: 0.6796 (m-80) REVERT: A 1120 ILE cc_start: 0.8797 (mp) cc_final: 0.8560 (pt) REVERT: A 1122 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7979 (tp40) REVERT: A 1136 ASP cc_start: 0.7966 (t0) cc_final: 0.7385 (p0) outliers start: 31 outliers final: 27 residues processed: 162 average time/residue: 0.0780 time to fit residues: 18.2318 Evaluate side-chains 159 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain A residue 1216 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.220551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.177479 restraints weight = 11847.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174543 restraints weight = 10137.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.175607 restraints weight = 11392.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.176690 restraints weight = 6702.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.178339 restraints weight = 5572.752| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9784 Z= 0.161 Angle : 0.593 8.396 13262 Z= 0.306 Chirality : 0.043 0.264 1538 Planarity : 0.004 0.036 1646 Dihedral : 4.556 18.677 1294 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.59 % Allowed : 15.93 % Favored : 81.48 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1187 helix: 1.03 (0.19), residues: 784 sheet: 1.25 (0.71), residues: 58 loop : 0.71 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1030 TYR 0.035 0.002 TYR A1259 PHE 0.033 0.002 PHE A 258 TRP 0.012 0.001 TRP A1099 HIS 0.003 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 9784) covalent geometry : angle 0.59325 / 0.31 (13262) hydrogen bonds : bond 0.04123 / 2.78 ( 609) hydrogen bonds : angle 4.37494 / 3.19 ( 1761) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8642 (tp40) cc_final: 0.8070 (tp-100) REVERT: A 276 MET cc_start: 0.7629 (mmm) cc_final: 0.7421 (mmm) REVERT: A 706 ARG cc_start: 0.7834 (tpp-160) cc_final: 0.7426 (mmt180) REVERT: A 744 MET cc_start: 0.7316 (mmm) cc_final: 0.7001 (mtt) REVERT: A 1016 TYR cc_start: 0.7589 (m-10) cc_final: 0.6814 (m-80) REVERT: A 1122 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7980 (tp40) REVERT: A 1136 ASP cc_start: 0.7895 (t0) cc_final: 0.7262 (p0) outliers start: 27 outliers final: 23 residues processed: 154 average time/residue: 0.0816 time to fit residues: 18.1042 Evaluate side-chains 154 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1216 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1183 GLN ** 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 = 0.4534 r_free = 0.4534 target = 0.218880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.174541 restraints weight = 11817.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.174421 restraints weight = 9965.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.174312 restraints weight = 10296.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.175220 restraints weight = 6238.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.175729 restraints weight = 5263.187| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9784 Z= 0.192 Angle : 0.625 9.662 13262 Z= 0.320 Chirality : 0.044 0.244 1538 Planarity : 0.004 0.035 1646 Dihedral : 4.588 19.028 1294 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.69 % Allowed : 16.70 % Favored : 80.61 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1187 helix: 0.94 (0.19), residues: 783 sheet: 1.27 (0.71), residues: 58 loop : 0.74 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1030 TYR 0.029 0.002 TYR A 289 PHE 0.034 0.002 PHE A 258 TRP 0.012 0.001 TRP A 947 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 ( 9784) covalent geometry : angle 0.62493 / 0.32 (13262) hydrogen bonds : bond 0.04286 / 2.89 ( 609) hydrogen bonds : angle 4.45366 / 3.24 ( 1761) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8633 (tp40) cc_final: 0.8109 (tp-100) REVERT: A 276 MET cc_start: 0.7703 (mmm) cc_final: 0.7479 (mmm) REVERT: A 289 TYR cc_start: 0.8226 (m-80) cc_final: 0.7886 (m-80) REVERT: A 706 ARG cc_start: 0.7860 (tpp-160) cc_final: 0.7459 (mmt180) REVERT: A 744 MET cc_start: 0.7192 (mmm) cc_final: 0.6865 (mtt) REVERT: A 1016 TYR cc_start: 0.7646 (m-10) cc_final: 0.6850 (m-80) REVERT: A 1136 ASP cc_start: 0.7759 (t0) cc_final: 0.7173 (p0) outliers start: 28 outliers final: 25 residues processed: 154 average time/residue: 0.0755 time to fit residues: 16.6292 Evaluate side-chains 154 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1216 GLN Chi-restraints excluded: chain A residue 1272 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 82 optimal weight: 0.4980 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 725 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.221983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.178143 restraints weight = 11807.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.177126 restraints weight = 10390.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.177765 restraints weight = 9806.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.178764 restraints weight = 6234.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.179184 restraints weight = 5227.897| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9784 Z= 0.138 Angle : 0.577 10.199 13262 Z= 0.297 Chirality : 0.041 0.192 1538 Planarity : 0.003 0.036 1646 Dihedral : 4.467 18.381 1294 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.78 % Allowed : 16.60 % Favored : 80.61 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.25), residues: 1187 helix: 1.09 (0.19), residues: 785 sheet: 1.40 (0.70), residues: 58 loop : 0.80 (0.37), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1030 TYR 0.028 0.002 TYR A 289 PHE 0.032 0.001 PHE A 258 TRP 0.013 0.001 TRP A 25 HIS 0.003 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9784) covalent geometry : angle 0.57681 / 0.30 (13262) hydrogen bonds : bond 0.03965 / 2.66 ( 609) hydrogen bonds : angle 4.29453 / 3.13 ( 1761) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1318.94 seconds wall clock time: 23 minutes 33.01 seconds (1413.01 seconds total)