Starting phenix.real_space_refine on Sat Aug 23 05:39:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i4a_35167/08_2025/8i4a_35167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i4a_35167/08_2025/8i4a_35167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i4a_35167/08_2025/8i4a_35167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i4a_35167/08_2025/8i4a_35167.map" model { file = "/net/cci-nas-00/data/ceres_data/8i4a_35167/08_2025/8i4a_35167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i4a_35167/08_2025/8i4a_35167.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6340 2.51 5 N 1645 2.21 5 O 1735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 9763 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1218, 9727 Classifications: {'peptide': 1218} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1178} Chain breaks: 2 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'H9F': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.03, per 1000 atoms: 0.21 Number of scatterers: 9763 At special positions: 0 Unit cell: (77.04, 114.49, 146.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1735 8.00 N 1645 7.00 C 6340 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 259.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2306 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 5 sheets defined 66.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 37 Processing helix chain 'A' and resid 52 through 75 Processing helix chain 'A' and resid 79 through 93 removed outlier: 3.708A pdb=" N ALA A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 122 Proline residue: A 110 - end of helix removed outlier: 3.596A pdb=" N ASN A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 150 removed outlier: 3.519A pdb=" N ILE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 179 removed outlier: 4.012A pdb=" N HIS A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.591A pdb=" N LYS A 188 " --> pdb=" O MET A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 removed outlier: 3.665A pdb=" N ASN A 200 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 4.346A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N HIS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 218 through 234 removed outlier: 3.687A pdb=" N THR A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 removed outlier: 4.108A pdb=" N ALA A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix Processing helix chain 'A' and resid 257 through 263 removed outlier: 3.590A pdb=" N SER A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 282 removed outlier: 4.652A pdb=" N ALA A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.547A pdb=" N ILE A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 342 removed outlier: 3.788A pdb=" N PHE A 295 " --> pdb=" O TRP A 291 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 390 removed outlier: 3.896A pdb=" N PHE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Proline residue: A 370 - end of helix Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.901A pdb=" N VAL A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 529 through 533 removed outlier: 4.129A pdb=" N GLY A 532 " --> pdb=" O GLY A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 552 Processing helix chain 'A' and resid 566 through 577 Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.975A pdb=" N GLU A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 removed outlier: 3.790A pdb=" N TYR A 596 " --> pdb=" O GLN A 593 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.657A pdb=" N LEU A 630 " --> pdb=" O ASP A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 709 removed outlier: 4.051A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 709 " --> pdb=" O PHE A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 744 removed outlier: 3.724A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 804 removed outlier: 3.524A pdb=" N TYR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.758A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.764A pdb=" N ASP A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 861 removed outlier: 4.191A pdb=" N LEU A 841 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 844 " --> pdb=" O PHE A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 866 Processing helix chain 'A' and resid 872 through 884 Processing helix chain 'A' and resid 891 through 896 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.917A pdb=" N PHE A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 Processing helix chain 'A' and resid 920 through 932 Processing helix chain 'A' and resid 937 through 966 removed outlier: 3.969A pdb=" N SER A 945 " --> pdb=" O PHE A 941 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1017 removed outlier: 4.246A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1089 removed outlier: 3.918A pdb=" N SER A1086 " --> pdb=" O SER A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1113 Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1171 through 1175 Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1208 through 1223 removed outlier: 3.663A pdb=" N PHE A1223 " --> pdb=" O ILE A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1264 Processing helix chain 'A' and resid 1267 through 1275 Processing helix chain 'A' and resid 1278 through 1296 Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435 removed outlier: 6.824A pdb=" N GLN A 429 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR A 416 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU A 431 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 415 " --> pdb=" O HIS A 466 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N HIS A 466 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.643A pdb=" N ASP A 559 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR A 556 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL A 590 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 558 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 606 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 603 " --> pdb=" O LYS A 614 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS A 614 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA4, first strand: chain 'A' and resid 1056 through 1065 removed outlier: 6.919A pdb=" N VAL A1057 " --> pdb=" O MET A1049 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET A1049 " --> pdb=" O VAL A1057 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS A1059 " --> pdb=" O ASN A1047 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASN A1047 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU A1061 " --> pdb=" O ASN A1045 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N PHE A1043 " --> pdb=" O TRP A1099 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TRP A1099 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASN A1045 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS A1097 " --> pdb=" O ASN A1045 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1118 through 1120 removed outlier: 3.707A pdb=" N SER A1118 " --> pdb=" O ILE A1197 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL A1071 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS A1070 " --> pdb=" O LYS A1243 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N MET A1245 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1668 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: 1.23 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2977 1.33 - 1.46: 1849 1.46 - 1.58: 5079 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 9975 Sorted by residual: bond pdb=" C5 H9F A1401 " pdb=" N8 H9F A1401 " ideal model delta sigma weight residual 1.348 1.451 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C2 H9F A1401 " pdb=" N7 H9F A1401 " ideal model delta sigma weight residual 1.360 1.451 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C3 H9F A1401 " pdb=" N5 H9F A1401 " ideal model delta sigma weight residual 1.365 1.452 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C6 H9F A1401 " pdb=" N6 H9F A1401 " ideal model delta sigma weight residual 1.364 1.450 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C4 H9F A1401 " pdb=" C5 H9F A1401 " ideal model delta sigma weight residual 1.456 1.386 0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 9970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 13333 3.32 - 6.63: 165 6.63 - 9.95: 16 9.95 - 13.26: 0 13.26 - 16.58: 1 Bond angle restraints: 13515 Sorted by residual: angle pdb=" C LEU A 835 " pdb=" N LEU A 836 " pdb=" CA LEU A 836 " ideal model delta sigma weight residual 119.83 113.58 6.25 1.11e+00 8.12e-01 3.17e+01 angle pdb=" C LEU A 892 " pdb=" N GLU A 893 " pdb=" CA GLU A 893 " ideal model delta sigma weight residual 122.56 114.37 8.19 1.72e+00 3.38e-01 2.27e+01 angle pdb=" CA LEU A1214 " pdb=" CB LEU A1214 " pdb=" CG LEU A1214 " ideal model delta sigma weight residual 116.30 132.88 -16.58 3.50e+00 8.16e-02 2.24e+01 angle pdb=" N ILE A 805 " pdb=" CA ILE A 805 " pdb=" C ILE A 805 " ideal model delta sigma weight residual 113.42 108.41 5.01 1.17e+00 7.31e-01 1.84e+01 angle pdb=" C LYS A 305 " pdb=" N GLU A 306 " pdb=" CA GLU A 306 " ideal model delta sigma weight residual 121.92 114.56 7.36 1.73e+00 3.34e-01 1.81e+01 ... (remaining 13510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.63: 5593 23.63 - 47.26: 341 47.26 - 70.89: 32 70.89 - 94.52: 8 94.52 - 118.15: 3 Dihedral angle restraints: 5977 sinusoidal: 2418 harmonic: 3559 Sorted by residual: dihedral pdb=" CA PHE A 352 " pdb=" C PHE A 352 " pdb=" N VAL A 353 " pdb=" CA VAL A 353 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA CYS A 253 " pdb=" C CYS A 253 " pdb=" N PHE A 254 " pdb=" CA PHE A 254 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA TRP A 291 " pdb=" C TRP A 291 " pdb=" N GLU A 292 " pdb=" CA GLU A 292 " ideal model delta harmonic sigma weight residual -180.00 -159.01 -20.99 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 5974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1165 0.060 - 0.120: 346 0.120 - 0.179: 47 0.179 - 0.239: 2 0.239 - 0.299: 1 Chirality restraints: 1561 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CG LEU A 582 " pdb=" CB LEU A 582 " pdb=" CD1 LEU A 582 " pdb=" CD2 LEU A 582 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL A 889 " pdb=" CA VAL A 889 " pdb=" CG1 VAL A 889 " pdb=" CG2 VAL A 889 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1558 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 869 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO A 870 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 870 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 870 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 218 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO A 219 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 219 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 219 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1123 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO A1124 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A1124 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1124 " 0.029 5.00e-02 4.00e+02 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 241 2.67 - 3.23: 9944 3.23 - 3.79: 15184 3.79 - 4.34: 20372 4.34 - 4.90: 33410 Nonbonded interactions: 79151 Sorted by model distance: nonbonded pdb=" NH2 ARG A 272 " pdb=" O PHE A 825 " model vdw 2.115 3.120 nonbonded pdb=" OG SER A 794 " pdb=" OD1 ASP A 833 " model vdw 2.123 3.040 nonbonded pdb=" NE2 GLN A1183 " pdb=" O ALA A1203 " model vdw 2.137 3.120 nonbonded pdb=" O VAL A 410 " pdb=" OG1 THR A 434 " model vdw 2.210 3.040 nonbonded pdb=" OD1 ASP A 953 " pdb=" NE2 GLN A 994 " model vdw 2.227 3.120 ... (remaining 79146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.740 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.013 0.648 9976 Z= 0.810 Angle : 0.937 16.579 13515 Z= 0.503 Chirality : 0.055 0.299 1561 Planarity : 0.005 0.060 1676 Dihedral : 15.095 118.154 3671 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.46 (0.24), residues: 1212 helix: -0.84 (0.18), residues: 781 sheet: -1.03 (0.61), residues: 76 loop : -0.79 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1220 TYR 0.016 0.002 TYR A1016 PHE 0.036 0.003 PHE A 98 TRP 0.017 0.002 TRP A 64 HIS 0.008 0.001 HIS A1060 Details of bonding type rmsd covalent geometry : bond 0.01162 ( 9975) covalent geometry : angle 0.93721 (13515) hydrogen bonds : bond 0.15629 ( 573) hydrogen bonds : angle 7.07178 ( 1668) Misc. bond : bond 0.64828 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.246 Fit side-chains REVERT: A 611 MET cc_start: 0.4865 (tpt) cc_final: 0.3322 (tmm) REVERT: A 921 GLU cc_start: 0.8464 (pt0) cc_final: 0.8226 (pt0) REVERT: A 1049 MET cc_start: 0.8412 (mtp) cc_final: 0.7824 (mmm) REVERT: A 1069 GLU cc_start: 0.7498 (pt0) cc_final: 0.7177 (pt0) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0677 time to fit residues: 10.5174 Evaluate side-chains 85 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN A 387 GLN A 551 GLN A 845 GLN A1134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.210588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145115 restraints weight = 10776.784| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.17 r_work: 0.3053 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9976 Z= 0.231 Angle : 0.661 8.351 13515 Z= 0.341 Chirality : 0.045 0.163 1561 Planarity : 0.005 0.055 1676 Dihedral : 8.134 87.501 1350 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.75 % Allowed : 7.72 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.56 (0.24), residues: 1212 helix: -0.11 (0.19), residues: 801 sheet: -0.88 (0.61), residues: 76 loop : -0.47 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 915 TYR 0.013 0.002 TYR A 157 PHE 0.027 0.002 PHE A 324 TRP 0.013 0.001 TRP A 64 HIS 0.003 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 9975) covalent geometry : angle 0.66117 (13515) hydrogen bonds : bond 0.05367 ( 573) hydrogen bonds : angle 5.20144 ( 1668) Misc. bond : bond 0.00092 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.8626 (tpt) cc_final: 0.7878 (mmt) REVERT: A 387 GLN cc_start: 0.8849 (tp40) cc_final: 0.8638 (tp-100) REVERT: A 611 MET cc_start: 0.4906 (tpt) cc_final: 0.3801 (tmm) REVERT: A 1059 LYS cc_start: 0.7998 (tptp) cc_final: 0.7748 (tptp) REVERT: A 1069 GLU cc_start: 0.7504 (pt0) cc_final: 0.7221 (pt0) outliers start: 8 outliers final: 5 residues processed: 111 average time/residue: 0.0839 time to fit residues: 13.4872 Evaluate side-chains 105 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1168 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 60 optimal weight: 40.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 GLN A 994 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.213515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148968 restraints weight = 10564.697| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.04 r_work: 0.3075 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9976 Z= 0.150 Angle : 0.540 6.258 13515 Z= 0.282 Chirality : 0.041 0.155 1561 Planarity : 0.004 0.051 1676 Dihedral : 7.393 89.912 1350 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.79 % Allowed : 9.98 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.10 (0.25), residues: 1212 helix: 0.41 (0.19), residues: 801 sheet: -0.61 (0.62), residues: 76 loop : -0.27 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.013 0.001 TYR A 157 PHE 0.020 0.001 PHE A 324 TRP 0.010 0.001 TRP A1147 HIS 0.003 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9975) covalent geometry : angle 0.54001 (13515) hydrogen bonds : bond 0.04566 ( 573) hydrogen bonds : angle 4.71241 ( 1668) Misc. bond : bond 0.00071 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.6902 (tpt) cc_final: 0.6670 (ttt) REVERT: A 307 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7391 (mm) REVERT: A 387 GLN cc_start: 0.8697 (tp40) cc_final: 0.8492 (tp-100) REVERT: A 763 TRP cc_start: 0.8768 (t60) cc_final: 0.8433 (t60) REVERT: A 893 GLU cc_start: 0.8598 (pp20) cc_final: 0.8080 (tm-30) REVERT: A 1049 MET cc_start: 0.8507 (mtm) cc_final: 0.8088 (mtt) REVERT: A 1059 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7784 (tptp) REVERT: A 1097 LYS cc_start: 0.7432 (mptt) cc_final: 0.6931 (mtmt) REVERT: A 1131 MET cc_start: 0.7689 (tpp) cc_final: 0.7363 (tpp) outliers start: 19 outliers final: 10 residues processed: 123 average time/residue: 0.0761 time to fit residues: 13.8507 Evaluate side-chains 116 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1016 TYR Chi-restraints excluded: chain A residue 1059 LYS Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 58 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.216634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.152789 restraints weight = 10571.096| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.17 r_work: 0.3099 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9976 Z= 0.113 Angle : 0.493 6.404 13515 Z= 0.256 Chirality : 0.039 0.147 1561 Planarity : 0.003 0.046 1676 Dihedral : 6.925 88.774 1350 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.79 % Allowed : 11.58 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.59 (0.25), residues: 1212 helix: 0.80 (0.19), residues: 800 sheet: -0.42 (0.62), residues: 76 loop : -0.13 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 824 TYR 0.013 0.001 TYR A1016 PHE 0.016 0.001 PHE A 324 TRP 0.010 0.001 TRP A 912 HIS 0.002 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9975) covalent geometry : angle 0.49329 (13515) hydrogen bonds : bond 0.03949 ( 573) hydrogen bonds : angle 4.35352 ( 1668) Misc. bond : bond 0.00099 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 186 MET cc_start: 0.6961 (tpt) cc_final: 0.6730 (ttt) REVERT: A 307 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7188 (mm) REVERT: A 611 MET cc_start: 0.4739 (tpt) cc_final: 0.3453 (tmm) REVERT: A 763 TRP cc_start: 0.8820 (t60) cc_final: 0.8433 (t60) REVERT: A 820 ARG cc_start: 0.8026 (mtm110) cc_final: 0.7805 (ttp80) REVERT: A 1059 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7608 (tptp) REVERT: A 1097 LYS cc_start: 0.7225 (mptt) cc_final: 0.6805 (mtpp) REVERT: A 1131 MET cc_start: 0.7764 (tpp) cc_final: 0.7431 (tpp) outliers start: 19 outliers final: 15 residues processed: 119 average time/residue: 0.0826 time to fit residues: 14.4641 Evaluate side-chains 120 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1016 TYR Chi-restraints excluded: chain A residue 1059 LYS Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 108 optimal weight: 0.5980 chunk 44 optimal weight: 40.0000 chunk 88 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.214237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.149530 restraints weight = 10581.176| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.20 r_work: 0.3087 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9976 Z= 0.123 Angle : 0.508 7.489 13515 Z= 0.260 Chirality : 0.040 0.150 1561 Planarity : 0.003 0.047 1676 Dihedral : 6.754 87.507 1350 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.17 % Allowed : 13.09 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.82 (0.25), residues: 1212 helix: 0.96 (0.19), residues: 800 sheet: -0.28 (0.60), residues: 76 loop : -0.01 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 915 TYR 0.011 0.001 TYR A1016 PHE 0.013 0.001 PHE A 325 TRP 0.009 0.001 TRP A 763 HIS 0.002 0.000 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9975) covalent geometry : angle 0.50765 (13515) hydrogen bonds : bond 0.03996 ( 573) hydrogen bonds : angle 4.28096 ( 1668) Misc. bond : bond 0.00111 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 307 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7301 (mm) REVERT: A 611 MET cc_start: 0.4865 (tpt) cc_final: 0.3669 (tmm) REVERT: A 836 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7550 (mp) REVERT: A 909 GLN cc_start: 0.7152 (mt0) cc_final: 0.6945 (mt0) REVERT: A 1059 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7598 (tptp) REVERT: A 1097 LYS cc_start: 0.7172 (mptt) cc_final: 0.6796 (mtpp) outliers start: 23 outliers final: 17 residues processed: 119 average time/residue: 0.0831 time to fit residues: 14.2126 Evaluate side-chains 122 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1016 TYR Chi-restraints excluded: chain A residue 1059 LYS Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 51 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.213591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126518 restraints weight = 10648.548| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.23 r_work: 0.3120 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9976 Z= 0.127 Angle : 0.510 7.549 13515 Z= 0.261 Chirality : 0.040 0.149 1561 Planarity : 0.003 0.048 1676 Dihedral : 6.660 86.877 1350 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.45 % Allowed : 14.03 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.95 (0.25), residues: 1212 helix: 1.06 (0.19), residues: 801 sheet: -0.18 (0.59), residues: 76 loop : 0.04 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 815 TYR 0.010 0.001 TYR A1016 PHE 0.013 0.001 PHE A 325 TRP 0.016 0.001 TRP A 763 HIS 0.002 0.000 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9975) covalent geometry : angle 0.50958 (13515) hydrogen bonds : bond 0.03977 ( 573) hydrogen bonds : angle 4.22536 ( 1668) Misc. bond : bond 0.00112 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8102 (m-30) REVERT: A 292 GLU cc_start: 0.8138 (pt0) cc_final: 0.7882 (pt0) REVERT: A 307 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7438 (mm) REVERT: A 611 MET cc_start: 0.4807 (tpt) cc_final: 0.3530 (tmm) REVERT: A 763 TRP cc_start: 0.8892 (t60) cc_final: 0.8684 (t60) REVERT: A 836 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7545 (mp) REVERT: A 1059 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7559 (tptp) REVERT: A 1097 LYS cc_start: 0.7313 (mptt) cc_final: 0.6967 (mtmt) REVERT: A 1131 MET cc_start: 0.7788 (tpp) cc_final: 0.7554 (tpp) outliers start: 26 outliers final: 20 residues processed: 118 average time/residue: 0.0808 time to fit residues: 13.9753 Evaluate side-chains 122 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1016 TYR Chi-restraints excluded: chain A residue 1059 LYS Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 80 optimal weight: 0.5980 chunk 3 optimal weight: 0.0060 chunk 109 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.216089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.151724 restraints weight = 10599.318| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.14 r_work: 0.3091 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9976 Z= 0.114 Angle : 0.494 8.429 13515 Z= 0.252 Chirality : 0.039 0.147 1561 Planarity : 0.003 0.048 1676 Dihedral : 6.558 86.321 1350 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.45 % Allowed : 14.22 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.11 (0.25), residues: 1212 helix: 1.19 (0.19), residues: 801 sheet: -0.22 (0.54), residues: 86 loop : 0.10 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 815 TYR 0.011 0.001 TYR A1016 PHE 0.012 0.001 PHE A 325 TRP 0.013 0.001 TRP A 763 HIS 0.002 0.000 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9975) covalent geometry : angle 0.49393 (13515) hydrogen bonds : bond 0.03813 ( 573) hydrogen bonds : angle 4.12275 ( 1668) Misc. bond : bond 0.00096 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.374 Fit side-chains REVERT: A 74 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8138 (m-30) REVERT: A 307 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7284 (mm) REVERT: A 387 GLN cc_start: 0.8691 (tp40) cc_final: 0.8469 (tp-100) REVERT: A 836 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7440 (mp) REVERT: A 1059 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7515 (tptp) REVERT: A 1097 LYS cc_start: 0.7331 (mptt) cc_final: 0.6987 (mtmt) outliers start: 26 outliers final: 19 residues processed: 119 average time/residue: 0.0834 time to fit residues: 14.8434 Evaluate side-chains 118 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1016 TYR Chi-restraints excluded: chain A residue 1059 LYS Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 78 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.215578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151258 restraints weight = 10641.261| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.19 r_work: 0.3080 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9976 Z= 0.121 Angle : 0.518 9.416 13515 Z= 0.263 Chirality : 0.040 0.167 1561 Planarity : 0.004 0.058 1676 Dihedral : 6.545 86.154 1350 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.35 % Allowed : 15.07 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.17 (0.25), residues: 1212 helix: 1.23 (0.19), residues: 798 sheet: -0.18 (0.54), residues: 86 loop : 0.15 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1220 TYR 0.011 0.001 TYR A1016 PHE 0.012 0.001 PHE A 325 TRP 0.013 0.001 TRP A 763 HIS 0.002 0.000 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9975) covalent geometry : angle 0.51790 (13515) hydrogen bonds : bond 0.03891 ( 573) hydrogen bonds : angle 4.15057 ( 1668) Misc. bond : bond 0.00096 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.371 Fit side-chains REVERT: A 74 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: A 307 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7316 (mm) REVERT: A 611 MET cc_start: 0.4984 (tpt) cc_final: 0.3831 (tmm) REVERT: A 836 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7402 (mp) REVERT: A 1059 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7433 (tptp) REVERT: A 1097 LYS cc_start: 0.7423 (mptt) cc_final: 0.6979 (mtpp) REVERT: A 1131 MET cc_start: 0.7810 (tpp) cc_final: 0.7545 (tpp) REVERT: A 1220 ARG cc_start: 0.7734 (mpt90) cc_final: 0.7385 (mpt90) outliers start: 25 outliers final: 20 residues processed: 111 average time/residue: 0.0870 time to fit residues: 14.3111 Evaluate side-chains 120 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1016 TYR Chi-restraints excluded: chain A residue 1059 LYS Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 50.0000 chunk 68 optimal weight: 0.4980 chunk 41 optimal weight: 0.0270 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.0010 chunk 30 optimal weight: 0.8980 overall best weight: 0.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.216012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.152108 restraints weight = 10584.675| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.31 r_work: 0.3093 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9976 Z= 0.104 Angle : 0.512 9.737 13515 Z= 0.257 Chirality : 0.039 0.150 1561 Planarity : 0.003 0.046 1676 Dihedral : 6.445 85.452 1350 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.07 % Allowed : 15.63 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.31 (0.25), residues: 1212 helix: 1.34 (0.19), residues: 800 sheet: -0.09 (0.54), residues: 86 loop : 0.19 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 815 TYR 0.012 0.001 TYR A1016 PHE 0.011 0.001 PHE A 325 TRP 0.014 0.001 TRP A 763 HIS 0.003 0.000 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9975) covalent geometry : angle 0.51202 (13515) hydrogen bonds : bond 0.03706 ( 573) hydrogen bonds : angle 4.06140 ( 1668) Misc. bond : bond 0.00083 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.378 Fit side-chains REVERT: A 74 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: A 231 MET cc_start: 0.8343 (mtt) cc_final: 0.7910 (mtm) REVERT: A 307 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7208 (mm) REVERT: A 611 MET cc_start: 0.4786 (tpt) cc_final: 0.3507 (tmm) REVERT: A 763 TRP cc_start: 0.8915 (t60) cc_final: 0.8551 (t60) REVERT: A 890 LYS cc_start: 0.7904 (ttmt) cc_final: 0.7528 (tttm) REVERT: A 912 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.7413 (t60) REVERT: A 1097 LYS cc_start: 0.7472 (mptt) cc_final: 0.7035 (mtpp) REVERT: A 1131 MET cc_start: 0.7684 (tpp) cc_final: 0.7408 (tpp) REVERT: A 1220 ARG cc_start: 0.7694 (mpt90) cc_final: 0.7263 (mpt90) outliers start: 22 outliers final: 19 residues processed: 118 average time/residue: 0.0926 time to fit residues: 16.0492 Evaluate side-chains 120 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1016 TYR Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 117 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 78 optimal weight: 0.0050 chunk 45 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 20.0000 chunk 16 optimal weight: 0.5980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.215457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132242 restraints weight = 10552.971| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.97 r_work: 0.3113 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9976 Z= 0.111 Angle : 0.540 11.157 13515 Z= 0.269 Chirality : 0.040 0.201 1561 Planarity : 0.003 0.046 1676 Dihedral : 6.408 85.077 1350 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.17 % Allowed : 15.73 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.43 (0.25), residues: 1212 helix: 1.43 (0.19), residues: 800 sheet: 0.24 (0.61), residues: 71 loop : 0.12 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 815 TYR 0.011 0.001 TYR A1016 PHE 0.011 0.001 PHE A 325 TRP 0.013 0.001 TRP A 763 HIS 0.004 0.001 HIS A1060 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9975) covalent geometry : angle 0.54006 (13515) hydrogen bonds : bond 0.03729 ( 573) hydrogen bonds : angle 4.08306 ( 1668) Misc. bond : bond 0.00083 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.330 Fit side-chains REVERT: A 74 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.7831 (t0) REVERT: A 231 MET cc_start: 0.8382 (mtt) cc_final: 0.8075 (mtp) REVERT: A 307 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7152 (mm) REVERT: A 611 MET cc_start: 0.4709 (tpt) cc_final: 0.3444 (tmm) REVERT: A 763 TRP cc_start: 0.8906 (t60) cc_final: 0.8520 (t60) REVERT: A 890 LYS cc_start: 0.7865 (ttmt) cc_final: 0.7486 (tttm) REVERT: A 1097 LYS cc_start: 0.7473 (mptt) cc_final: 0.7025 (mtpp) REVERT: A 1131 MET cc_start: 0.7667 (tpp) cc_final: 0.7405 (tpp) REVERT: A 1220 ARG cc_start: 0.7658 (mpt90) cc_final: 0.7224 (mpt90) outliers start: 23 outliers final: 21 residues processed: 114 average time/residue: 0.0817 time to fit residues: 13.7442 Evaluate side-chains 120 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1016 TYR Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 115 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 38 optimal weight: 0.0170 chunk 43 optimal weight: 40.0000 chunk 88 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 30.0000 chunk 94 optimal weight: 4.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.214980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132048 restraints weight = 10562.747| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.90 r_work: 0.3128 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 9976 Z= 0.189 Angle : 0.877 59.197 13515 Z= 0.496 Chirality : 0.042 0.569 1561 Planarity : 0.003 0.045 1676 Dihedral : 6.397 85.082 1350 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.07 % Allowed : 15.91 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.43 (0.25), residues: 1212 helix: 1.44 (0.19), residues: 800 sheet: 0.24 (0.61), residues: 71 loop : 0.12 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 915 TYR 0.011 0.001 TYR A1016 PHE 0.011 0.001 PHE A 325 TRP 0.013 0.001 TRP A 763 HIS 0.018 0.001 HIS A1060 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9975) covalent geometry : angle 0.87701 (13515) hydrogen bonds : bond 0.03741 ( 573) hydrogen bonds : angle 4.08240 ( 1668) Misc. bond : bond 0.00084 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2327.43 seconds wall clock time: 40 minutes 38.63 seconds (2438.63 seconds total)