Starting phenix.real_space_refine on Fri Feb 14 09:33:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i4a_35167/02_2025/8i4a_35167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i4a_35167/02_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_35167/02_2025/8i4a_35167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i4a_35167/02_2025/8i4a_35167.map" model { file = "/net/cci-nas-00/data/ceres_data/8i4a_35167/02_2025/8i4a_35167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i4a_35167/02_2025/8i4a_35167.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.90, per 1000 atoms: 0.60 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: 2.55 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.26 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: 3.40 Time building geometry restraints manager: 2.88 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.940 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.490 ------------------------------------------------------------------------------- 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 : 0.012 0.103 9975 Z= 0.750 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 : 13.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (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 TRP 0.017 0.002 TRP A 64 HIS 0.008 0.001 HIS A1060 PHE 0.036 0.003 PHE A 98 TYR 0.016 0.002 TYR A1016 ARG 0.010 0.001 ARG A1220 *********************** 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 : 1.097 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: 0.1935 time to fit residues: 29.8411 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 : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 A1134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.211788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125549 restraints weight = 10583.519| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.68 r_work: 0.3104 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9975 Z= 0.275 Angle : 0.624 8.398 13515 Z= 0.322 Chirality : 0.043 0.158 1561 Planarity : 0.004 0.054 1676 Dihedral : 8.082 87.537 1350 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.56 % Allowed : 6.69 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.25), residues: 1212 helix: -0.00 (0.19), residues: 801 sheet: -0.83 (0.61), residues: 76 loop : -0.42 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 912 HIS 0.003 0.001 HIS A 152 PHE 0.024 0.002 PHE A 324 TYR 0.015 0.001 TYR A 157 ARG 0.004 0.000 ARG A 272 *********************** 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: 6 poor density : 112 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.8575 (tpt) cc_final: 0.7863 (mmt) REVERT: A 387 GLN cc_start: 0.8843 (tp40) cc_final: 0.8637 (tp-100) REVERT: A 611 MET cc_start: 0.4898 (tpt) cc_final: 0.3810 (tmm) REVERT: A 824 ARG cc_start: 0.8301 (mtt180) cc_final: 0.8052 (mtm-85) REVERT: A 893 GLU cc_start: 0.8702 (pp20) cc_final: 0.8272 (tm-30) REVERT: A 1049 MET cc_start: 0.8694 (mtp) cc_final: 0.8185 (mtt) REVERT: A 1059 LYS cc_start: 0.7991 (tptp) cc_final: 0.7761 (tptp) REVERT: A 1069 GLU cc_start: 0.7584 (pt0) cc_final: 0.7296 (pt0) outliers start: 6 outliers final: 4 residues processed: 112 average time/residue: 0.2144 time to fit residues: 34.7797 Evaluate side-chains 104 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 25 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 551 GLN A 845 GLN A 909 GLN A 994 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.206382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119492 restraints weight = 10744.592| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.62 r_work: 0.3038 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9975 Z= 0.415 Angle : 0.642 7.120 13515 Z= 0.333 Chirality : 0.045 0.161 1561 Planarity : 0.004 0.053 1676 Dihedral : 7.600 88.429 1350 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.07 % Allowed : 10.55 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1212 helix: 0.10 (0.19), residues: 804 sheet: -0.66 (0.61), residues: 76 loop : -0.29 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.003 0.001 HIS A 152 PHE 0.021 0.002 PHE A 324 TYR 0.012 0.002 TYR A 985 ARG 0.004 0.000 ARG A 167 *********************** 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 123 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7667 (mm) REVERT: A 387 GLN cc_start: 0.8835 (tp40) cc_final: 0.8629 (tp-100) REVERT: A 1049 MET cc_start: 0.8698 (mtp) cc_final: 0.8405 (mtm) REVERT: A 1112 ASP cc_start: 0.8654 (m-30) cc_final: 0.7391 (p0) REVERT: A 1131 MET cc_start: 0.7657 (tpp) cc_final: 0.7331 (tpp) REVERT: A 1245 MET cc_start: 0.8696 (mmt) cc_final: 0.8492 (mmm) outliers start: 22 outliers final: 15 residues processed: 111 average time/residue: 0.2149 time to fit residues: 35.2977 Evaluate side-chains 112 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 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 393 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1168 THR 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 25 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4313 r_free = 0.4313 target = 0.212865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.148606 restraints weight = 10545.675| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.11 r_work: 0.3061 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9975 Z= 0.204 Angle : 0.528 6.426 13515 Z= 0.273 Chirality : 0.041 0.268 1561 Planarity : 0.004 0.051 1676 Dihedral : 7.199 88.054 1350 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.79 % Allowed : 12.24 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1212 helix: 0.55 (0.19), residues: 803 sheet: -0.53 (0.62), residues: 76 loop : -0.25 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.002 0.000 HIS A 35 PHE 0.016 0.001 PHE A 324 TYR 0.017 0.001 TYR A1016 ARG 0.002 0.000 ARG A 915 *********************** 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 129 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 611 MET cc_start: 0.4848 (tpt) cc_final: 0.3505 (tmm) REVERT: A 807 LYS cc_start: 0.9001 (mttt) cc_final: 0.8545 (mtpp) REVERT: A 836 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7549 (mp) REVERT: A 1097 LYS cc_start: 0.7410 (mptt) cc_final: 0.6857 (mtpp) REVERT: A 1131 MET cc_start: 0.7620 (tpp) cc_final: 0.7273 (tpp) outliers start: 19 outliers final: 13 residues processed: 117 average time/residue: 0.2174 time to fit residues: 36.6983 Evaluate side-chains 111 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 101 ILE Chi-restraints excluded: chain A residue 237 CYS 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 836 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 1220 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 46 optimal weight: 0.0050 chunk 100 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.215486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150650 restraints weight = 10454.627| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.14 r_work: 0.3074 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9975 Z= 0.168 Angle : 0.504 7.319 13515 Z= 0.260 Chirality : 0.040 0.146 1561 Planarity : 0.003 0.050 1676 Dihedral : 6.888 89.014 1350 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.26 % Allowed : 13.37 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1212 helix: 0.83 (0.19), residues: 803 sheet: -0.37 (0.60), residues: 76 loop : -0.08 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 912 HIS 0.002 0.000 HIS A 35 PHE 0.014 0.001 PHE A 325 TYR 0.016 0.001 TYR A1016 ARG 0.003 0.000 ARG A 915 *********************** 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 129 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7010 (t80) cc_final: 0.6798 (t80) REVERT: A 307 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7305 (mm) REVERT: A 611 MET cc_start: 0.4804 (tpt) cc_final: 0.3603 (tmm) REVERT: A 763 TRP cc_start: 0.8774 (t60) cc_final: 0.8424 (t60) REVERT: A 807 LYS cc_start: 0.8985 (mttt) cc_final: 0.8509 (mtpp) REVERT: A 820 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7799 (ttp80) REVERT: A 836 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7505 (mp) REVERT: A 1097 LYS cc_start: 0.7378 (mptt) cc_final: 0.6888 (mtpp) REVERT: A 1131 MET cc_start: 0.7901 (tpp) cc_final: 0.7596 (tpp) outliers start: 24 outliers final: 17 residues processed: 119 average time/residue: 0.1971 time to fit residues: 34.2751 Evaluate side-chains 120 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 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 1084 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1187 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 17 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 74 optimal weight: 0.0980 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4340 r_free = 0.4340 target = 0.215743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130051 restraints weight = 10494.761| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.60 r_work: 0.3100 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9975 Z= 0.176 Angle : 0.505 7.667 13515 Z= 0.258 Chirality : 0.040 0.147 1561 Planarity : 0.003 0.050 1676 Dihedral : 6.704 87.224 1350 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.45 % Allowed : 13.84 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1212 helix: 1.00 (0.19), residues: 803 sheet: -0.21 (0.60), residues: 76 loop : 0.02 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1147 HIS 0.002 0.000 HIS A 35 PHE 0.013 0.001 PHE A 325 TYR 0.016 0.001 TYR A1016 ARG 0.003 0.000 ARG A 915 *********************** 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 135 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.000 Fit side-chains REVERT: A 74 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7377 (t0) REVERT: A 292 GLU cc_start: 0.8135 (pt0) cc_final: 0.7925 (pt0) REVERT: A 307 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7220 (mm) REVERT: A 611 MET cc_start: 0.4838 (tpt) cc_final: 0.3608 (tmm) REVERT: A 706 ARG cc_start: 0.8320 (tpt90) cc_final: 0.8116 (tpt170) REVERT: A 763 TRP cc_start: 0.8887 (t60) cc_final: 0.8366 (t60) REVERT: A 836 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7503 (mp) REVERT: A 1097 LYS cc_start: 0.7193 (mptt) cc_final: 0.6704 (mtpp) REVERT: A 1131 MET cc_start: 0.7813 (tpp) cc_final: 0.7557 (tpp) REVERT: A 1220 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7823 (mpt90) outliers start: 26 outliers final: 21 residues processed: 124 average time/residue: 0.1996 time to fit residues: 36.0976 Evaluate side-chains 128 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 1187 LEU 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 96 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4338 r_free = 0.4338 target = 0.215474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.128516 restraints weight = 10652.564| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.25 r_work: 0.3117 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9975 Z= 0.181 Angle : 0.501 8.084 13515 Z= 0.255 Chirality : 0.040 0.147 1561 Planarity : 0.003 0.050 1676 Dihedral : 6.610 86.637 1350 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.64 % Allowed : 14.31 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1212 helix: 1.13 (0.19), residues: 801 sheet: -0.03 (0.60), residues: 76 loop : 0.06 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.002 0.000 HIS A1060 PHE 0.013 0.001 PHE A 325 TYR 0.014 0.001 TYR A1016 ARG 0.004 0.000 ARG A 915 *********************** 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 135 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.994 Fit side-chains REVERT: A 74 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7375 (t0) REVERT: A 306 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7683 (pt0) REVERT: A 307 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7464 (mm) REVERT: A 387 GLN cc_start: 0.8834 (tp40) cc_final: 0.8358 (tt0) REVERT: A 763 TRP cc_start: 0.8904 (t60) cc_final: 0.8536 (t60) REVERT: A 836 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7488 (mp) REVERT: A 1097 LYS cc_start: 0.7408 (mptt) cc_final: 0.6910 (mtpp) REVERT: A 1131 MET cc_start: 0.7820 (tpp) cc_final: 0.7566 (tpp) outliers start: 28 outliers final: 22 residues processed: 125 average time/residue: 0.2016 time to fit residues: 37.3464 Evaluate side-chains 125 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 101 ILE 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 306 GLU 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 1084 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 49 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 103 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.214936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127814 restraints weight = 10790.398| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.26 r_work: 0.3131 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9975 Z= 0.159 Angle : 0.510 9.489 13515 Z= 0.259 Chirality : 0.040 0.169 1561 Planarity : 0.004 0.059 1676 Dihedral : 6.557 86.089 1350 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.54 % Allowed : 15.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1212 helix: 1.25 (0.19), residues: 799 sheet: -0.01 (0.59), residues: 76 loop : 0.14 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 763 HIS 0.003 0.000 HIS A1060 PHE 0.012 0.001 PHE A 325 TYR 0.015 0.001 TYR A1016 ARG 0.010 0.000 ARG A1220 *********************** 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 129 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 1.133 Fit side-chains REVERT: A 74 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7368 (t0) REVERT: A 306 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.7730 (pt0) REVERT: A 307 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7314 (mm) REVERT: A 611 MET cc_start: 0.4968 (tpt) cc_final: 0.3836 (tmm) REVERT: A 763 TRP cc_start: 0.8842 (t60) cc_final: 0.8474 (t60) REVERT: A 836 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7428 (mp) REVERT: A 1097 LYS cc_start: 0.7391 (mptt) cc_final: 0.6902 (mtpp) REVERT: A 1131 MET cc_start: 0.7836 (tpp) cc_final: 0.7581 (tpp) REVERT: A 1220 ARG cc_start: 0.7709 (mpt90) cc_final: 0.7421 (mpt90) outliers start: 27 outliers final: 22 residues processed: 119 average time/residue: 0.2170 time to fit residues: 38.9784 Evaluate side-chains 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 101 ILE 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 306 GLU 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 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 33 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 84 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4330 r_free = 0.4330 target = 0.214721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.128230 restraints weight = 10642.403| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.21 r_work: 0.3137 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9975 Z= 0.165 Angle : 0.518 9.779 13515 Z= 0.260 Chirality : 0.039 0.144 1561 Planarity : 0.003 0.049 1676 Dihedral : 6.518 85.751 1350 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.64 % Allowed : 15.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1212 helix: 1.28 (0.19), residues: 799 sheet: -0.00 (0.58), residues: 76 loop : 0.17 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 763 HIS 0.002 0.000 HIS A1060 PHE 0.012 0.001 PHE A 325 TYR 0.015 0.001 TYR A1016 ARG 0.005 0.000 ARG A 915 *********************** 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 129 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7129 (mtp) cc_final: 0.6746 (ttt) REVERT: A 74 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7373 (t0) REVERT: A 306 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7729 (pt0) REVERT: A 307 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7360 (mm) REVERT: A 611 MET cc_start: 0.4852 (tpt) cc_final: 0.3637 (tmm) REVERT: A 763 TRP cc_start: 0.8870 (t60) cc_final: 0.8522 (t60) REVERT: A 836 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.6941 (tp) REVERT: A 1097 LYS cc_start: 0.7518 (mptt) cc_final: 0.6997 (mtpp) REVERT: A 1131 MET cc_start: 0.7831 (tpp) cc_final: 0.7594 (tpp) REVERT: A 1220 ARG cc_start: 0.7706 (mpt90) cc_final: 0.7356 (mpt90) outliers start: 28 outliers final: 24 residues processed: 118 average time/residue: 0.2047 time to fit residues: 35.2267 Evaluate side-chains 125 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 101 ILE 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 306 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 345 VAL 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 393 ASP 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 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 20 optimal weight: 0.0970 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 0.3980 chunk 35 optimal weight: 0.4980 chunk 114 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.4340 r_free = 0.4340 target = 0.215721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.129171 restraints weight = 10636.726| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.24 r_work: 0.3146 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9975 Z= 0.154 Angle : 0.516 10.768 13515 Z= 0.259 Chirality : 0.039 0.143 1561 Planarity : 0.003 0.048 1676 Dihedral : 6.439 85.088 1350 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.45 % Allowed : 16.01 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1212 helix: 1.40 (0.19), residues: 800 sheet: 0.15 (0.59), residues: 76 loop : 0.23 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 763 HIS 0.003 0.000 HIS A1060 PHE 0.011 0.001 PHE A 325 TYR 0.014 0.001 TYR A1016 ARG 0.007 0.000 ARG A 815 ********************** 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 128 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.6976 (mtp) cc_final: 0.6661 (ttt) REVERT: A 74 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7446 (t0) REVERT: A 76 GLN cc_start: 0.7364 (pt0) cc_final: 0.7097 (pt0) REVERT: A 231 MET cc_start: 0.8369 (mtt) cc_final: 0.7941 (mtm) REVERT: A 306 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7192 (pt0) REVERT: A 307 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7348 (mm) REVERT: A 611 MET cc_start: 0.4650 (tpt) cc_final: 0.3359 (tmm) REVERT: A 763 TRP cc_start: 0.8871 (t60) cc_final: 0.8488 (t60) REVERT: A 890 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7573 (tttm) REVERT: A 1097 LYS cc_start: 0.7499 (mptt) cc_final: 0.6992 (mtpp) REVERT: A 1131 MET cc_start: 0.7750 (tpp) cc_final: 0.7533 (tpp) REVERT: A 1220 ARG cc_start: 0.7697 (mpt90) cc_final: 0.7359 (mpt90) outliers start: 26 outliers final: 20 residues processed: 118 average time/residue: 0.2074 time to fit residues: 35.8649 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 : 1.035 ------------------------------------------------------------------------------- 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 101 ILE 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 306 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 345 VAL 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 926 LEU Chi-restraints excluded: chain A residue 1006 MET 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 18 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.210488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125667 restraints weight = 10718.308| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.79 r_work: 0.3042 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9975 Z= 0.369 Angle : 0.611 10.546 13515 Z= 0.310 Chirality : 0.044 0.163 1561 Planarity : 0.004 0.048 1676 Dihedral : 6.738 88.714 1350 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.64 % Allowed : 15.63 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1212 helix: 0.96 (0.19), residues: 803 sheet: 0.02 (0.59), residues: 76 loop : 0.19 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.009 0.001 HIS A1060 PHE 0.015 0.002 PHE A 325 TYR 0.018 0.002 TYR A1016 ARG 0.006 0.000 ARG A 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6007.57 seconds wall clock time: 107 minutes 4.10 seconds (6424.10 seconds total)