Starting phenix.real_space_refine on Sat Aug 23 18:15:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x01_37964/08_2025/8x01_37964.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x01_37964/08_2025/8x01_37964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x01_37964/08_2025/8x01_37964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x01_37964/08_2025/8x01_37964.map" model { file = "/net/cci-nas-00/data/ceres_data/8x01_37964/08_2025/8x01_37964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x01_37964/08_2025/8x01_37964.cif" } resolution = 3.01 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= -0.002 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1404 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 81 5.16 5 C 8105 2.51 5 N 2182 2.21 5 O 2372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12742 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 10782 Classifications: {'peptide': 1350} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 67, 'TRANS': 1282} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 517 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "C" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 642 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "D" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain: "E" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 412 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9139 SG CYS A1187 15.673 94.179 45.655 1.00113.77 S ATOM 9164 SG CYS A1190 17.319 93.253 42.205 1.00110.61 S ATOM 8797 SG CYS A1142 26.288 109.947 52.146 1.00 76.21 S ATOM 10502 SG CYS A1379 23.718 109.223 50.767 1.00105.36 S ATOM 10508 SG CYS A1380 26.618 106.383 52.254 1.00 96.09 S Time building chain proxies: 2.53, per 1000 atoms: 0.20 Number of scatterers: 12742 At special positions: 0 Unit cell: (126.14, 138.33, 134.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 81 16.00 O 2372 8.00 N 2182 7.00 C 8105 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: 0.78 Conformation dependent library (CDL) restraints added in 427.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A1372 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A1374 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1190 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1187 " pdb=" ZN A3002 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1142 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1380 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1379 " Number of angles added : 2 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3070 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 8 sheets defined 61.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 removed outlier: 3.645A pdb=" N LEU A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.547A pdb=" N GLY A 42 " --> pdb=" O PRO A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.555A pdb=" N GLN A 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 55 removed outlier: 3.509A pdb=" N ILE A 52 " --> pdb=" O ASN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 74 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 90 through 98 removed outlier: 4.040A pdb=" N LEU A 95 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 108 through 122 Processing helix chain 'A' and resid 124 through 141 Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 175 through 198 Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 265 through 285 removed outlier: 4.246A pdb=" N ARG A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.960A pdb=" N ILE A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 330 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 361 through 362 No H-bonds generated for 'chain 'A' and resid 361 through 362' Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.907A pdb=" N ARG A 366 " --> pdb=" O CYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.629A pdb=" N LYS A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 413 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 430 through 440 Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.648A pdb=" N LYS A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 Processing helix chain 'A' and resid 467 through 471 removed outlier: 4.426A pdb=" N ASP A 471 " --> pdb=" O PRO A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 3.642A pdb=" N LYS A 477 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 4.118A pdb=" N VAL A 491 " --> pdb=" O TRP A 488 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 492 " --> pdb=" O MET A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 505 removed outlier: 4.527A pdb=" N GLN A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 568 through 585 removed outlier: 3.636A pdb=" N HIS A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 590 Processing helix chain 'A' and resid 598 through 611 Processing helix chain 'A' and resid 671 through 677 removed outlier: 4.014A pdb=" N CYS A 674 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 675 " --> pdb=" O LYS A 672 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP A 677 " --> pdb=" O CYS A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 694 Proline residue: A 684 - end of helix Processing helix chain 'A' and resid 700 through 709 removed outlier: 3.999A pdb=" N ARG A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 768 Processing helix chain 'A' and resid 794 through 820 removed outlier: 4.202A pdb=" N LEU A 808 " --> pdb=" O LYS A 804 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE A 809 " --> pdb=" O ALA A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 858 removed outlier: 3.800A pdb=" N ASN A 855 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 887 Processing helix chain 'A' and resid 890 through 912 Processing helix chain 'A' and resid 920 through 929 removed outlier: 3.546A pdb=" N HIS A 929 " --> pdb=" O ALA A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 939 removed outlier: 3.549A pdb=" N ILE A 933 " --> pdb=" O HIS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 944 Processing helix chain 'A' and resid 951 through 955 Processing helix chain 'A' and resid 961 through 977 Processing helix chain 'A' and resid 980 through 989 removed outlier: 3.659A pdb=" N LEU A 984 " --> pdb=" O ASP A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1003 removed outlier: 3.533A pdb=" N LEU A1000 " --> pdb=" O LYS A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1031 Processing helix chain 'A' and resid 1033 through 1037 Processing helix chain 'A' and resid 1043 through 1057 Processing helix chain 'A' and resid 1062 through 1073 Processing helix chain 'A' and resid 1073 through 1084 Processing helix chain 'A' and resid 1088 through 1099 Processing helix chain 'A' and resid 1102 through 1111 Processing helix chain 'A' and resid 1111 through 1122 removed outlier: 3.748A pdb=" N GLU A1122 " --> pdb=" O SER A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1137 removed outlier: 3.564A pdb=" N ALA A1136 " --> pdb=" O PHE A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1155 Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1171 through 1176 removed outlier: 3.659A pdb=" N VAL A1176 " --> pdb=" O PRO A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1192 Processing helix chain 'A' and resid 1242 through 1260 Processing helix chain 'A' and resid 1262 through 1275 removed outlier: 3.515A pdb=" N GLU A1271 " --> pdb=" O GLN A1267 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1272 " --> pdb=" O ASP A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1288 Processing helix chain 'A' and resid 1338 through 1358 Processing helix chain 'B' and resid 219 through 245 Processing helix chain 'B' and resid 246 through 276 removed outlier: 3.828A pdb=" N THR B 258 " --> pdb=" O ASN B 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 272 removed outlier: 4.122A pdb=" N GLY C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N MET C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA C 244 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 243 removed outlier: 3.704A pdb=" N LEU D 243 " --> pdb=" O VAL D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 267 removed outlier: 4.620A pdb=" N MET D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 265 " --> pdb=" O THR D 261 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 266 " --> pdb=" O THR D 262 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 271 removed outlier: 3.556A pdb=" N ALA E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.206A pdb=" N TYR A 234 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 390 through 393 Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AA4, first strand: chain 'A' and resid 563 through 566 Processing sheet with id=AA5, first strand: chain 'A' and resid 780 through 790 Processing sheet with id=AA6, first strand: chain 'A' and resid 835 through 838 removed outlier: 3.617A pdb=" N PHE A 836 " --> pdb=" O PHE A 843 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1180 through 1182 Processing sheet with id=AA8, first strand: chain 'A' and resid 1206 through 1207 removed outlier: 3.890A pdb=" N ILE A1206 " --> pdb=" O SER A1365 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2055 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: 1.89 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2108 1.31 - 1.44: 3226 1.44 - 1.56: 7510 1.56 - 1.69: 0 1.69 - 1.81: 133 Bond restraints: 12977 Sorted by residual: bond pdb=" C GLU A 554 " pdb=" N LYS A 555 " ideal model delta sigma weight residual 1.331 1.433 -0.102 1.36e-02 5.41e+03 5.61e+01 bond pdb=" C SER A 774 " pdb=" N MET A 775 " ideal model delta sigma weight residual 1.329 1.240 0.089 1.23e-02 6.61e+03 5.18e+01 bond pdb=" C GLU A 56 " pdb=" N SER A 57 " ideal model delta sigma weight residual 1.335 1.246 0.089 1.38e-02 5.25e+03 4.15e+01 bond pdb=" C LYS A 555 " pdb=" N GLU A 556 " ideal model delta sigma weight residual 1.331 1.246 0.084 1.34e-02 5.57e+03 3.94e+01 bond pdb=" C PHE C 293 " pdb=" N SER C 294 " ideal model delta sigma weight residual 1.333 1.250 0.084 1.34e-02 5.57e+03 3.90e+01 ... (remaining 12972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 17289 2.66 - 5.32: 267 5.32 - 7.99: 29 7.99 - 10.65: 4 10.65 - 13.31: 2 Bond angle restraints: 17591 Sorted by residual: angle pdb=" N LEU A 361 " pdb=" CA LEU A 361 " pdb=" C LEU A 361 " ideal model delta sigma weight residual 112.30 98.99 13.31 1.36e+00 5.41e-01 9.58e+01 angle pdb=" O SER A 774 " pdb=" C SER A 774 " pdb=" N MET A 775 " ideal model delta sigma weight residual 122.85 114.90 7.95 1.14e+00 7.69e-01 4.86e+01 angle pdb=" N LEU A 362 " pdb=" CA LEU A 362 " pdb=" C LEU A 362 " ideal model delta sigma weight residual 112.92 104.45 8.47 1.23e+00 6.61e-01 4.75e+01 angle pdb=" CA SER C 301 " pdb=" C SER C 301 " pdb=" N GLY C 302 " ideal model delta sigma weight residual 119.46 115.44 4.02 6.10e-01 2.69e+00 4.35e+01 angle pdb=" O GLU A 56 " pdb=" C GLU A 56 " pdb=" N SER A 57 " ideal model delta sigma weight residual 122.55 115.11 7.44 1.24e+00 6.50e-01 3.60e+01 ... (remaining 17586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 6920 17.78 - 35.57: 804 35.57 - 53.35: 181 53.35 - 71.13: 38 71.13 - 88.91: 7 Dihedral angle restraints: 7950 sinusoidal: 3234 harmonic: 4716 Sorted by residual: dihedral pdb=" CA LEU A 849 " pdb=" C LEU A 849 " pdb=" N THR A 850 " pdb=" CA THR A 850 " ideal model delta harmonic sigma weight residual -180.00 -158.24 -21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" C THR A 181 " pdb=" N THR A 181 " pdb=" CA THR A 181 " pdb=" CB THR A 181 " ideal model delta harmonic sigma weight residual -122.00 -111.64 -10.36 0 2.50e+00 1.60e-01 1.72e+01 dihedral pdb=" CA ILE A 865 " pdb=" C ILE A 865 " pdb=" N LEU A 866 " pdb=" CA LEU A 866 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 7947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1628 0.050 - 0.101: 317 0.101 - 0.151: 90 0.151 - 0.202: 23 0.202 - 0.252: 3 Chirality restraints: 2061 Sorted by residual: chirality pdb=" CA MET B 269 " pdb=" N MET B 269 " pdb=" C MET B 269 " pdb=" CB MET B 269 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ILE A 460 " pdb=" N ILE A 460 " pdb=" C ILE A 460 " pdb=" CB ILE A 460 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CG LEU C 243 " pdb=" CB LEU C 243 " pdb=" CD1 LEU C 243 " pdb=" CD2 LEU C 243 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2058 not shown) Planarity restraints: 2226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 358 " 0.028 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C THR A 358 " -0.094 2.00e-02 2.50e+03 pdb=" O THR A 358 " 0.035 2.00e-02 2.50e+03 pdb=" N ALA A 359 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 777 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C GLN A 777 " 0.070 2.00e-02 2.50e+03 pdb=" O GLN A 777 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY A 778 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 301 " -0.018 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C SER C 301 " 0.066 2.00e-02 2.50e+03 pdb=" O SER C 301 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY C 302 " -0.023 2.00e-02 2.50e+03 ... (remaining 2223 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2889 2.79 - 3.32: 12814 3.32 - 3.84: 21679 3.84 - 4.37: 25664 4.37 - 4.90: 43566 Nonbonded interactions: 106612 Sorted by model distance: nonbonded pdb=" NE2 HIS A 13 " pdb=" O THR A 862 " model vdw 2.259 3.120 nonbonded pdb=" OG SER A 952 " pdb=" OD1 ASP A1171 " model vdw 2.273 3.040 nonbonded pdb=" NH2 ARG A 841 " pdb=" O LEU A 849 " model vdw 2.279 3.120 nonbonded pdb=" OH TYR A 534 " pdb=" OD2 ASP A 543 " model vdw 2.283 3.040 nonbonded pdb=" N GLN A1131 " pdb=" OE1 GLN A1131 " model vdw 2.298 3.120 ... (remaining 106607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'E' and resid 218 through 267) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.210 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.005 0.102 12984 Z= 0.322 Angle : 0.746 13.309 17593 Z= 0.493 Chirality : 0.048 0.252 2061 Planarity : 0.005 0.073 2226 Dihedral : 15.840 88.914 4880 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.49 % Allowed : 19.14 % Favored : 80.38 % Cbeta Deviations : 0.07 % 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 aren not related in a simple way. whole: 1.10 (0.21), residues: 1588 helix: 1.51 (0.17), residues: 889 sheet: -0.36 (0.61), residues: 81 loop : -0.18 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 231 TYR 0.014 0.001 TYR A 289 PHE 0.022 0.001 PHE A 564 TRP 0.012 0.001 TRP A 982 HIS 0.003 0.001 HIS A 697 Details of bonding type rmsd covalent geometry : bond 0.00469 (12977) covalent geometry : angle 0.74599 (17591) hydrogen bonds : bond 0.12953 ( 718) hydrogen bonds : angle 5.48531 ( 2055) metal coordination : bond 0.00392 ( 7) metal coordination : angle 1.61680 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 243 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7806 (mttt) REVERT: A 810 PHE cc_start: 0.8324 (t80) cc_final: 0.8060 (t80) REVERT: A 1043 ASN cc_start: 0.7319 (p0) cc_final: 0.6599 (p0) REVERT: E 238 LYS cc_start: 0.8363 (pttm) cc_final: 0.7681 (ptmt) outliers start: 7 outliers final: 3 residues processed: 245 average time/residue: 0.1122 time to fit residues: 38.6624 Evaluate side-chains 214 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 211 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 1263 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 816 ASN A1008 ASN C 234 HIS E 254 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.159608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122578 restraints weight = 16937.406| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.19 r_work: 0.3352 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12984 Z= 0.141 Angle : 0.593 13.476 17593 Z= 0.297 Chirality : 0.042 0.191 2061 Planarity : 0.005 0.053 2226 Dihedral : 4.040 35.667 1740 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.95 % Allowed : 19.21 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.21), residues: 1588 helix: 1.84 (0.17), residues: 907 sheet: -0.36 (0.61), residues: 79 loop : -0.03 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 687 TYR 0.015 0.001 TYR A 289 PHE 0.021 0.001 PHE A 394 TRP 0.011 0.001 TRP A 982 HIS 0.010 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00325 (12977) covalent geometry : angle 0.59138 (17591) hydrogen bonds : bond 0.04423 ( 718) hydrogen bonds : angle 4.42710 ( 2055) metal coordination : bond 0.00395 ( 7) metal coordination : angle 4.62280 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 TRP cc_start: 0.8318 (OUTLIER) cc_final: 0.8085 (t-100) REVERT: A 381 LYS cc_start: 0.7833 (mmmt) cc_final: 0.7270 (mttt) REVERT: A 539 GLU cc_start: 0.7677 (tp30) cc_final: 0.7344 (tp30) REVERT: A 810 PHE cc_start: 0.7944 (t80) cc_final: 0.7675 (t80) REVERT: A 1043 ASN cc_start: 0.6878 (p0) cc_final: 0.6166 (p0) REVERT: B 231 ARG cc_start: 0.8842 (mtp180) cc_final: 0.8531 (mtm180) REVERT: B 267 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7770 (tm-30) REVERT: E 238 LYS cc_start: 0.8340 (pttm) cc_final: 0.7670 (ptmt) REVERT: E 252 ILE cc_start: 0.9045 (tp) cc_final: 0.8731 (tt) outliers start: 28 outliers final: 14 residues processed: 255 average time/residue: 0.1135 time to fit residues: 40.6049 Evaluate side-chains 224 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 249 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 152 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 GLN A 818 HIS A 871 GLN A1120 ASN B 233 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.154875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117828 restraints weight = 17213.556| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.20 r_work: 0.3282 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12984 Z= 0.207 Angle : 0.618 10.390 17593 Z= 0.315 Chirality : 0.044 0.182 2061 Planarity : 0.005 0.061 2226 Dihedral : 4.216 37.996 1735 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.92 % Allowed : 18.86 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.21), residues: 1588 helix: 1.69 (0.17), residues: 908 sheet: -0.55 (0.60), residues: 79 loop : -0.10 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 231 TYR 0.019 0.002 TYR A 289 PHE 0.012 0.002 PHE A 699 TRP 0.014 0.002 TRP A 182 HIS 0.008 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00503 (12977) covalent geometry : angle 0.61676 (17591) hydrogen bonds : bond 0.04830 ( 718) hydrogen bonds : angle 4.45789 ( 2055) metal coordination : bond 0.00814 ( 7) metal coordination : angle 3.17841 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7542 (mttt) REVERT: A 435 GLU cc_start: 0.7791 (mp0) cc_final: 0.7481 (mp0) REVERT: A 1043 ASN cc_start: 0.7128 (p0) cc_final: 0.6578 (p0) REVERT: B 267 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7720 (tm-30) REVERT: B 286 VAL cc_start: 0.7215 (t) cc_final: 0.6954 (p) REVERT: D 248 MET cc_start: 0.5008 (tmm) cc_final: 0.4382 (tpp) outliers start: 42 outliers final: 31 residues processed: 239 average time/residue: 0.1034 time to fit residues: 35.2972 Evaluate side-chains 231 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1404 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 265 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 158 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 152 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 956 ASN A1120 ASN B 233 GLN B 245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.157525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.121002 restraints weight = 17201.684| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.15 r_work: 0.3332 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12984 Z= 0.134 Angle : 0.579 12.634 17593 Z= 0.294 Chirality : 0.042 0.289 2061 Planarity : 0.004 0.070 2226 Dihedral : 4.065 35.548 1735 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.57 % Allowed : 19.55 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.21), residues: 1588 helix: 1.77 (0.17), residues: 910 sheet: -0.60 (0.60), residues: 79 loop : -0.07 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1078 TYR 0.015 0.001 TYR A 289 PHE 0.026 0.001 PHE A 394 TRP 0.013 0.001 TRP A 982 HIS 0.005 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00311 (12977) covalent geometry : angle 0.57831 (17591) hydrogen bonds : bond 0.04307 ( 718) hydrogen bonds : angle 4.31744 ( 2055) metal coordination : bond 0.00418 ( 7) metal coordination : angle 2.73376 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8996 (OUTLIER) cc_final: 0.8391 (t-100) REVERT: A 381 LYS cc_start: 0.7990 (mmmt) cc_final: 0.7487 (mttt) REVERT: A 539 GLU cc_start: 0.7843 (tp30) cc_final: 0.7406 (tp30) REVERT: A 707 MET cc_start: 0.9205 (mtm) cc_final: 0.8995 (mtt) REVERT: A 810 PHE cc_start: 0.8071 (t80) cc_final: 0.7796 (t80) REVERT: A 1043 ASN cc_start: 0.7103 (p0) cc_final: 0.6572 (p0) REVERT: B 228 MET cc_start: 0.8608 (mmm) cc_final: 0.8365 (mmm) REVERT: B 274 LYS cc_start: 0.8656 (tttm) cc_final: 0.8256 (ttmm) outliers start: 37 outliers final: 29 residues processed: 237 average time/residue: 0.1148 time to fit residues: 38.5834 Evaluate side-chains 230 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 249 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A1120 ASN B 233 GLN ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.156499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120191 restraints weight = 17319.643| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.16 r_work: 0.3326 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12984 Z= 0.148 Angle : 0.592 11.481 17593 Z= 0.298 Chirality : 0.042 0.167 2061 Planarity : 0.004 0.064 2226 Dihedral : 4.035 24.172 1735 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.34 % Allowed : 20.04 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.21), residues: 1588 helix: 1.77 (0.17), residues: 911 sheet: -0.65 (0.59), residues: 79 loop : -0.09 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 788 TYR 0.017 0.001 TYR A 289 PHE 0.011 0.001 PHE A 404 TRP 0.012 0.001 TRP A 182 HIS 0.005 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00352 (12977) covalent geometry : angle 0.59191 (17591) hydrogen bonds : bond 0.04323 ( 718) hydrogen bonds : angle 4.29683 ( 2055) metal coordination : bond 0.00495 ( 7) metal coordination : angle 2.42813 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.9010 (OUTLIER) cc_final: 0.8335 (t-100) REVERT: A 381 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7507 (mttt) REVERT: A 539 GLU cc_start: 0.7914 (tp30) cc_final: 0.7419 (tp30) REVERT: A 601 LYS cc_start: 0.7125 (tttt) cc_final: 0.6882 (ptmt) REVERT: A 707 MET cc_start: 0.9248 (mtm) cc_final: 0.9025 (mtt) REVERT: A 771 ARG cc_start: 0.7747 (ttp-170) cc_final: 0.7434 (tmm160) REVERT: A 810 PHE cc_start: 0.8080 (t80) cc_final: 0.7801 (t80) REVERT: A 1043 ASN cc_start: 0.7164 (p0) cc_final: 0.6536 (p0) REVERT: B 274 LYS cc_start: 0.8629 (tttm) cc_final: 0.8255 (ttmm) REVERT: B 286 VAL cc_start: 0.7299 (t) cc_final: 0.7062 (p) outliers start: 48 outliers final: 34 residues processed: 239 average time/residue: 0.1069 time to fit residues: 35.9604 Evaluate side-chains 238 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1404 MET Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 265 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 122 optimal weight: 0.0770 chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 146 optimal weight: 0.0570 chunk 147 optimal weight: 0.6980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 956 ASN E 233 GLN E 254 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.159213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122683 restraints weight = 17187.349| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.18 r_work: 0.3361 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12984 Z= 0.117 Angle : 0.593 12.459 17593 Z= 0.292 Chirality : 0.041 0.178 2061 Planarity : 0.004 0.065 2226 Dihedral : 3.880 22.826 1733 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.64 % Allowed : 20.88 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.21), residues: 1588 helix: 1.94 (0.17), residues: 903 sheet: -0.62 (0.60), residues: 79 loop : 0.01 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 231 TYR 0.014 0.001 TYR A 289 PHE 0.013 0.001 PHE A1133 TRP 0.014 0.001 TRP A 982 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00259 (12977) covalent geometry : angle 0.59207 (17591) hydrogen bonds : bond 0.04090 ( 718) hydrogen bonds : angle 4.18621 ( 2055) metal coordination : bond 0.00314 ( 7) metal coordination : angle 2.23065 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8981 (OUTLIER) cc_final: 0.8404 (t-100) REVERT: A 381 LYS cc_start: 0.7970 (mmmt) cc_final: 0.7488 (mttt) REVERT: A 431 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7764 (mmmt) REVERT: A 459 ARG cc_start: 0.7248 (ttm-80) cc_final: 0.6717 (mmt-90) REVERT: A 539 GLU cc_start: 0.7885 (tp30) cc_final: 0.7348 (tp30) REVERT: A 707 MET cc_start: 0.9207 (mtm) cc_final: 0.8969 (mtt) REVERT: A 771 ARG cc_start: 0.7747 (ttp-170) cc_final: 0.7450 (tmm160) REVERT: A 810 PHE cc_start: 0.8062 (t80) cc_final: 0.7790 (t80) REVERT: A 1043 ASN cc_start: 0.7158 (p0) cc_final: 0.6539 (p0) REVERT: B 257 SER cc_start: 0.9206 (t) cc_final: 0.8879 (p) REVERT: D 248 MET cc_start: 0.5148 (tmm) cc_final: 0.4454 (tpt) outliers start: 38 outliers final: 26 residues processed: 243 average time/residue: 0.1111 time to fit residues: 38.2925 Evaluate side-chains 235 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 265 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 139 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 111 optimal weight: 0.2980 chunk 154 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A1120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.158731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.122533 restraints weight = 17322.724| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.18 r_work: 0.3354 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12984 Z= 0.127 Angle : 0.607 12.986 17593 Z= 0.301 Chirality : 0.042 0.199 2061 Planarity : 0.004 0.060 2226 Dihedral : 3.919 22.979 1733 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.06 % Allowed : 20.81 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.21), residues: 1588 helix: 1.88 (0.17), residues: 905 sheet: -0.62 (0.59), residues: 79 loop : -0.00 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 231 TYR 0.016 0.001 TYR A 289 PHE 0.017 0.001 PHE A 319 TRP 0.012 0.001 TRP A 982 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00292 (12977) covalent geometry : angle 0.60670 (17591) hydrogen bonds : bond 0.04104 ( 718) hydrogen bonds : angle 4.20749 ( 2055) metal coordination : bond 0.00419 ( 7) metal coordination : angle 2.00938 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8987 (OUTLIER) cc_final: 0.8252 (t-100) REVERT: A 381 LYS cc_start: 0.7995 (mmmt) cc_final: 0.7524 (mttt) REVERT: A 431 LYS cc_start: 0.8150 (mmmm) cc_final: 0.7820 (mmmt) REVERT: A 539 GLU cc_start: 0.7910 (tp30) cc_final: 0.7359 (tp30) REVERT: A 707 MET cc_start: 0.9202 (mtm) cc_final: 0.8968 (mtt) REVERT: A 771 ARG cc_start: 0.7786 (ttp-170) cc_final: 0.7507 (tmm160) REVERT: A 810 PHE cc_start: 0.8054 (t80) cc_final: 0.7779 (t80) REVERT: A 1043 ASN cc_start: 0.7165 (p0) cc_final: 0.6546 (p0) REVERT: B 257 SER cc_start: 0.9168 (t) cc_final: 0.8877 (p) outliers start: 44 outliers final: 39 residues processed: 236 average time/residue: 0.1315 time to fit residues: 43.9171 Evaluate side-chains 241 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1404 MET Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 255 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 41 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN E 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.158510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121825 restraints weight = 17189.364| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.20 r_work: 0.3345 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12984 Z= 0.135 Angle : 0.634 13.842 17593 Z= 0.315 Chirality : 0.043 0.188 2061 Planarity : 0.004 0.062 2226 Dihedral : 3.952 23.287 1733 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.13 % Allowed : 20.81 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.21), residues: 1588 helix: 1.85 (0.17), residues: 903 sheet: -0.62 (0.60), residues: 79 loop : -0.00 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 231 TYR 0.016 0.001 TYR A 289 PHE 0.014 0.001 PHE A1133 TRP 0.012 0.001 TRP A 182 HIS 0.005 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00313 (12977) covalent geometry : angle 0.63405 (17591) hydrogen bonds : bond 0.04178 ( 718) hydrogen bonds : angle 4.24419 ( 2055) metal coordination : bond 0.00438 ( 7) metal coordination : angle 2.00318 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 210 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8994 (OUTLIER) cc_final: 0.8255 (t-100) REVERT: A 381 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7498 (mttt) REVERT: A 431 LYS cc_start: 0.8141 (mmmm) cc_final: 0.7803 (mmmt) REVERT: A 539 GLU cc_start: 0.7918 (tp30) cc_final: 0.7354 (tp30) REVERT: A 707 MET cc_start: 0.9171 (mtm) cc_final: 0.8931 (mtt) REVERT: A 771 ARG cc_start: 0.7769 (ttp-170) cc_final: 0.7490 (tmm160) REVERT: A 810 PHE cc_start: 0.8022 (t80) cc_final: 0.7752 (t80) REVERT: A 1043 ASN cc_start: 0.7159 (p0) cc_final: 0.6537 (p0) REVERT: B 231 ARG cc_start: 0.8754 (mtm180) cc_final: 0.8382 (ptp-170) REVERT: B 257 SER cc_start: 0.9177 (t) cc_final: 0.8896 (p) REVERT: C 248 MET cc_start: 0.7751 (ppp) cc_final: 0.7456 (ppp) outliers start: 45 outliers final: 35 residues processed: 237 average time/residue: 0.1285 time to fit residues: 42.7039 Evaluate side-chains 240 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 249 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 0.0770 chunk 70 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 130 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 0.2980 chunk 79 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A1120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.160417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124026 restraints weight = 17260.365| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.20 r_work: 0.3367 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12984 Z= 0.119 Angle : 0.640 15.188 17593 Z= 0.319 Chirality : 0.043 0.195 2061 Planarity : 0.004 0.059 2226 Dihedral : 3.876 22.337 1733 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.51 % Allowed : 21.36 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.21), residues: 1588 helix: 1.92 (0.18), residues: 899 sheet: -0.61 (0.60), residues: 79 loop : 0.07 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 231 TYR 0.015 0.001 TYR A 289 PHE 0.011 0.001 PHE A 319 TRP 0.013 0.001 TRP A 982 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00260 (12977) covalent geometry : angle 0.64008 (17591) hydrogen bonds : bond 0.04094 ( 718) hydrogen bonds : angle 4.21254 ( 2055) metal coordination : bond 0.00309 ( 7) metal coordination : angle 1.98708 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8968 (OUTLIER) cc_final: 0.8241 (t-100) REVERT: A 381 LYS cc_start: 0.7970 (mmmt) cc_final: 0.7484 (mttt) REVERT: A 431 LYS cc_start: 0.8119 (mmmm) cc_final: 0.7769 (mmmt) REVERT: A 459 ARG cc_start: 0.7163 (ttm-80) cc_final: 0.6792 (mmt-90) REVERT: A 539 GLU cc_start: 0.7905 (tp30) cc_final: 0.7340 (tp30) REVERT: A 771 ARG cc_start: 0.7758 (ttp-170) cc_final: 0.7485 (tmm160) REVERT: A 810 PHE cc_start: 0.8002 (t80) cc_final: 0.7732 (t80) REVERT: A 1043 ASN cc_start: 0.7138 (p0) cc_final: 0.6530 (p0) REVERT: B 235 LEU cc_start: 0.8909 (mm) cc_final: 0.8667 (mp) REVERT: B 257 SER cc_start: 0.9224 (t) cc_final: 0.8936 (p) REVERT: C 248 MET cc_start: 0.7724 (ppp) cc_final: 0.7433 (ppp) outliers start: 36 outliers final: 29 residues processed: 239 average time/residue: 0.1285 time to fit residues: 43.0059 Evaluate side-chains 234 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1404 MET Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 255 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 93 optimal weight: 0.0050 chunk 62 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 118 optimal weight: 0.0010 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.161040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.124591 restraints weight = 17385.302| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.21 r_work: 0.3380 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12984 Z= 0.121 Angle : 0.700 22.934 17593 Z= 0.338 Chirality : 0.043 0.190 2061 Planarity : 0.004 0.059 2226 Dihedral : 3.885 21.584 1733 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.09 % Allowed : 22.20 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.21), residues: 1588 helix: 1.92 (0.18), residues: 894 sheet: -0.64 (0.59), residues: 79 loop : 0.08 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 231 TYR 0.015 0.001 TYR A 289 PHE 0.014 0.001 PHE A1133 TRP 0.013 0.001 TRP A 982 HIS 0.007 0.001 HIS A1374 Details of bonding type rmsd covalent geometry : bond 0.00262 (12977) covalent geometry : angle 0.69951 (17591) hydrogen bonds : bond 0.04094 ( 718) hydrogen bonds : angle 4.20502 ( 2055) metal coordination : bond 0.00431 ( 7) metal coordination : angle 2.89356 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.8960 (OUTLIER) cc_final: 0.8147 (t-100) REVERT: A 381 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7470 (mttt) REVERT: A 431 LYS cc_start: 0.8095 (mmmm) cc_final: 0.7757 (mmmt) REVERT: A 459 ARG cc_start: 0.7105 (ttm-80) cc_final: 0.6753 (mmt-90) REVERT: A 539 GLU cc_start: 0.7901 (tp30) cc_final: 0.7344 (tp30) REVERT: A 771 ARG cc_start: 0.7730 (ttp-170) cc_final: 0.7455 (tmm160) REVERT: A 810 PHE cc_start: 0.7986 (t80) cc_final: 0.7720 (t80) REVERT: A 999 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.8020 (p) REVERT: A 1043 ASN cc_start: 0.7120 (p0) cc_final: 0.6514 (p0) REVERT: B 257 SER cc_start: 0.9238 (t) cc_final: 0.8958 (p) REVERT: C 248 MET cc_start: 0.7770 (ppp) cc_final: 0.7516 (ppp) outliers start: 30 outliers final: 23 residues processed: 229 average time/residue: 0.1150 time to fit residues: 37.2691 Evaluate side-chains 229 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1404 MET Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 265 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 18 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 134 optimal weight: 0.0000 chunk 31 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A1283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.158321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.122523 restraints weight = 17316.685| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.29 r_work: 0.3334 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12984 Z= 0.148 Angle : 0.716 18.924 17593 Z= 0.348 Chirality : 0.044 0.242 2061 Planarity : 0.004 0.059 2226 Dihedral : 3.995 22.956 1733 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.95 % Allowed : 22.48 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.21), residues: 1588 helix: 1.79 (0.18), residues: 903 sheet: -0.66 (0.59), residues: 79 loop : 0.06 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 231 TYR 0.016 0.001 TYR A 289 PHE 0.012 0.001 PHE A 699 TRP 0.013 0.001 TRP A 182 HIS 0.007 0.001 HIS A1374 Details of bonding type rmsd covalent geometry : bond 0.00348 (12977) covalent geometry : angle 0.71486 (17591) hydrogen bonds : bond 0.04339 ( 718) hydrogen bonds : angle 4.30486 ( 2055) metal coordination : bond 0.00505 ( 7) metal coordination : angle 4.18047 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3945.03 seconds wall clock time: 68 minutes 7.80 seconds (4087.80 seconds total)