Starting phenix.real_space_refine on Sun Jun 8 18:49:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bwr_16295/06_2025/8bwr_16295.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bwr_16295/06_2025/8bwr_16295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bwr_16295/06_2025/8bwr_16295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bwr_16295/06_2025/8bwr_16295.map" model { file = "/net/cci-nas-00/data/ceres_data/8bwr_16295/06_2025/8bwr_16295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bwr_16295/06_2025/8bwr_16295.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6221 2.51 5 N 1602 2.21 5 O 1704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9570 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9545 Classifications: {'peptide': 1195} Link IDs: {'PTRANS': 37, 'TRANS': 1157} Chain breaks: 3 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.45, per 1000 atoms: 0.67 Number of scatterers: 9570 At special positions: 0 Unit cell: (74.048, 108.992, 143.936, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1704 8.00 N 1602 7.00 C 6221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2266 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 73.6% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.693A pdb=" N PHE A 23 " --> pdb=" O CYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 37 removed outlier: 3.771A pdb=" N LYS A 32 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 74 removed outlier: 3.627A pdb=" N PHE A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 122 removed outlier: 5.131A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.604A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 150 removed outlier: 3.600A pdb=" N LEU A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 180 removed outlier: 3.856A pdb=" N TYR A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 188 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 203 through 210 removed outlier: 3.982A pdb=" N GLN A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 234 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 236 through 290 removed outlier: 4.141A pdb=" N GLY A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.528A pdb=" N LYS A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ARG A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 342 removed outlier: 3.784A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 367 removed outlier: 4.151A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.552A pdb=" N VAL A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 452 removed outlier: 4.019A pdb=" N SER A 452 " --> pdb=" O ALA A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 449 through 452' Processing helix chain 'A' and resid 453 through 459 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 512 through 521 removed outlier: 3.649A pdb=" N ASP A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.652A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 697 through 707 removed outlier: 4.164A pdb=" N TYR A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 745 removed outlier: 3.771A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 745 " --> pdb=" O LYS A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 808 removed outlier: 4.006A pdb=" N GLY A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 806 " --> pdb=" O PHE A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 4.063A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 removed outlier: 3.564A pdb=" N ILE A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.806A pdb=" N LEU A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 861 removed outlier: 3.693A pdb=" N GLN A 849 " --> pdb=" O GLN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 910 removed outlier: 3.597A pdb=" N LEU A 868 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 869 " --> pdb=" O ALA A 865 " (cutoff:3.500A) Proline residue: A 870 - end of helix removed outlier: 3.754A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix Processing helix chain 'A' and resid 910 through 917 Processing helix chain 'A' and resid 919 through 970 removed outlier: 4.722A pdb=" N ILE A 955 " --> pdb=" O ARG A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1018 removed outlier: 3.687A pdb=" N GLY A 980 " --> pdb=" O ALA A 976 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 988 " --> pdb=" O SER A 984 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TRP A 995 " --> pdb=" O GLY A 991 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 997 " --> pdb=" O PHE A 993 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A1017 " --> pdb=" O VAL A1013 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1038 removed outlier: 3.894A pdb=" N GLU A1038 " --> pdb=" O TRP A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1089 removed outlier: 5.175A pdb=" N SER A1082 " --> pdb=" O GLY A1078 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N SER A1083 " --> pdb=" O ALA A1079 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A1084 " --> pdb=" O GLY A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1108 No H-bonds generated for 'chain 'A' and resid 1106 through 1108' Processing helix chain 'A' and resid 1109 through 1115 Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1171 through 1175 Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1202 through 1207 removed outlier: 3.671A pdb=" N ALA A1205 " --> pdb=" O GLU A1202 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN A1206 " --> pdb=" O ALA A1203 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A1207 " --> pdb=" O THR A1204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1202 through 1207' Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1234 through 1238 Processing helix chain 'A' and resid 1248 through 1251 Processing helix chain 'A' and resid 1257 through 1264 Processing helix chain 'A' and resid 1267 through 1275 Processing helix chain 'A' and resid 1276 through 1278 No H-bonds generated for 'chain 'A' and resid 1276 through 1278' Processing helix chain 'A' and resid 1279 through 1292 removed outlier: 3.618A pdb=" N ALA A1283 " --> pdb=" O ALA A1279 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A1291 " --> pdb=" O THR A1287 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A1292 " --> pdb=" O ALA A1288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 431 through 435 removed outlier: 5.330A pdb=" N LEU A 431 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 410 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.186A pdb=" N TYR A 556 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL A 590 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 558 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1056 through 1065 removed outlier: 6.583A pdb=" N VAL A1057 " --> pdb=" O MET A1049 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N MET A1049 " --> pdb=" O VAL A1057 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS A1059 " --> pdb=" O ASN A1047 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ASN A1047 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A1061 " --> pdb=" O ASN A1045 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL A1046 " --> pdb=" O GLU A1095 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU A1095 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1117 through 1120 removed outlier: 6.026A pdb=" N SER A1118 " --> pdb=" O ILE A1199 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A1243 " --> pdb=" O LYS A1070 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1815 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: 3.49 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1550 1.32 - 1.44: 2579 1.44 - 1.56: 5575 1.56 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 9774 Sorted by residual: bond pdb=" C7 P2E A1401 " pdb=" C8 P2E A1401 " ideal model delta sigma weight residual 1.529 1.480 0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" CB PHE A 843 " pdb=" CG PHE A 843 " ideal model delta sigma weight residual 1.502 1.451 0.051 2.30e-02 1.89e+03 4.86e+00 bond pdb=" CB PHE A 336 " pdb=" CG PHE A 336 " ideal model delta sigma weight residual 1.502 1.452 0.050 2.30e-02 1.89e+03 4.82e+00 bond pdb=" CB TRP A 291 " pdb=" CG TRP A 291 " ideal model delta sigma weight residual 1.498 1.430 0.068 3.10e-02 1.04e+03 4.76e+00 bond pdb=" CB PHE A 802 " pdb=" CG PHE A 802 " ideal model delta sigma weight residual 1.502 1.453 0.049 2.30e-02 1.89e+03 4.56e+00 ... (remaining 9769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 12686 2.03 - 4.06: 479 4.06 - 6.09: 58 6.09 - 8.12: 16 8.12 - 10.15: 5 Bond angle restraints: 13244 Sorted by residual: angle pdb=" N ASN A 28 " pdb=" CA ASN A 28 " pdb=" C ASN A 28 " ideal model delta sigma weight residual 109.81 117.75 -7.94 2.21e+00 2.05e-01 1.29e+01 angle pdb=" C LEU A 27 " pdb=" N ASN A 28 " pdb=" CA ASN A 28 " ideal model delta sigma weight residual 121.80 129.95 -8.15 2.44e+00 1.68e-01 1.11e+01 angle pdb=" N PHE A 205 " pdb=" CA PHE A 205 " pdb=" C PHE A 205 " ideal model delta sigma weight residual 111.82 115.57 -3.75 1.16e+00 7.43e-01 1.04e+01 angle pdb=" CA LEU A 357 " pdb=" CB LEU A 357 " pdb=" CG LEU A 357 " ideal model delta sigma weight residual 116.30 106.15 10.15 3.50e+00 8.16e-02 8.41e+00 angle pdb=" CA TYR A 881 " pdb=" CB TYR A 881 " pdb=" CG TYR A 881 " ideal model delta sigma weight residual 113.90 118.81 -4.91 1.80e+00 3.09e-01 7.43e+00 ... (remaining 13239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5355 17.56 - 35.12: 394 35.12 - 52.68: 77 52.68 - 70.24: 19 70.24 - 87.80: 8 Dihedral angle restraints: 5853 sinusoidal: 2359 harmonic: 3494 Sorted by residual: dihedral pdb=" CA ASP A 834 " pdb=" C ASP A 834 " pdb=" N LEU A 835 " pdb=" CA LEU A 835 " ideal model delta harmonic sigma weight residual -180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA VAL A1057 " pdb=" C VAL A1057 " pdb=" N LEU A1058 " pdb=" CA LEU A1058 " ideal model delta harmonic sigma weight residual 180.00 151.98 28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ARG A 37 " pdb=" C ARG A 37 " pdb=" N ARG A 38 " pdb=" CA ARG A 38 " ideal model delta harmonic sigma weight residual 180.00 152.85 27.15 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 5850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 936 0.044 - 0.088: 448 0.088 - 0.131: 131 0.131 - 0.175: 19 0.175 - 0.219: 7 Chirality restraints: 1541 Sorted by residual: chirality pdb=" C15 P2E A1401 " pdb=" C14 P2E A1401 " pdb=" C16 P2E A1401 " pdb=" O5 P2E A1401 " both_signs ideal model delta sigma weight residual False 2.23 2.44 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA HIS A 158 " pdb=" N HIS A 158 " pdb=" C HIS A 158 " pdb=" CB HIS A 158 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO A 110 " pdb=" N PRO A 110 " pdb=" C PRO A 110 " pdb=" CB PRO A 110 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 1538 not shown) Planarity restraints: 1644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 358 " 0.006 2.00e-02 2.50e+03 2.16e-02 9.29e+00 pdb=" CG TYR A 358 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 358 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 358 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 358 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR A 358 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 358 " 0.031 2.00e-02 2.50e+03 pdb=" OH TYR A 358 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 547 " 0.217 9.50e-02 1.11e+02 9.76e-02 6.79e+00 pdb=" NE ARG A 547 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 547 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 547 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 547 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 782 " -0.226 9.50e-02 1.11e+02 1.02e-01 6.42e+00 pdb=" NE ARG A 782 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 782 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 782 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 782 " -0.006 2.00e-02 2.50e+03 ... (remaining 1641 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1356 2.74 - 3.28: 10807 3.28 - 3.82: 15956 3.82 - 4.36: 19572 4.36 - 4.90: 31589 Nonbonded interactions: 79280 Sorted by model distance: nonbonded pdb=" O LYS A 498 " pdb=" OH TYR A 550 " model vdw 2.203 3.040 nonbonded pdb=" O ILE A 223 " pdb=" OG1 THR A 226 " model vdw 2.268 3.040 nonbonded pdb=" NH1 ARG A1076 " pdb=" OD1 ASP A1248 " model vdw 2.274 3.120 nonbonded pdb=" O ARG A1234 " pdb=" OG1 THR A1237 " model vdw 2.291 3.040 nonbonded pdb=" O ALA A 379 " pdb=" OG SER A 382 " model vdw 2.291 3.040 ... (remaining 79275 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.310 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.770 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.010 0.068 9774 Z= 0.428 Angle : 0.933 10.148 13244 Z= 0.499 Chirality : 0.053 0.219 1541 Planarity : 0.008 0.102 1644 Dihedral : 13.672 87.802 3587 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.96 % Allowed : 3.74 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.22), residues: 1187 helix: -1.43 (0.15), residues: 723 sheet: 0.25 (0.49), residues: 80 loop : -0.18 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A1025 HIS 0.015 0.002 HIS A 798 PHE 0.034 0.004 PHE A 336 TYR 0.032 0.004 TYR A 358 ARG 0.018 0.003 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.23996 ( 627) hydrogen bonds : angle 8.82135 ( 1815) covalent geometry : bond 0.00979 ( 9774) covalent geometry : angle 0.93300 (13244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 237 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TRP cc_start: 0.5585 (OUTLIER) cc_final: 0.5009 (t-100) REVERT: A 44 MET cc_start: 0.8220 (ptp) cc_final: 0.7446 (ptp) REVERT: A 143 PHE cc_start: 0.8136 (m-10) cc_final: 0.7274 (t80) REVERT: A 146 LEU cc_start: 0.7612 (mm) cc_final: 0.7381 (mm) REVERT: A 167 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8322 (ttt-90) REVERT: A 201 ASP cc_start: 0.8801 (t0) cc_final: 0.8545 (t0) REVERT: A 221 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7959 (tp-100) REVERT: A 258 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7915 (p90) REVERT: A 278 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7923 (mm-30) REVERT: A 309 LYS cc_start: 0.9206 (mttp) cc_final: 0.8895 (mttp) REVERT: A 312 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.8078 (tpt170) REVERT: A 336 PHE cc_start: 0.8580 (m-80) cc_final: 0.8266 (m-80) REVERT: A 352 PHE cc_start: 0.7713 (m-80) cc_final: 0.7401 (m-80) REVERT: A 363 LEU cc_start: 0.8541 (mm) cc_final: 0.8261 (mt) REVERT: A 368 PHE cc_start: 0.8882 (m-10) cc_final: 0.8636 (m-80) REVERT: A 387 GLN cc_start: 0.9159 (tt0) cc_final: 0.8753 (tt0) REVERT: A 505 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8218 (pt0) REVERT: A 711 TRP cc_start: 0.7228 (p-90) cc_final: 0.6979 (t-100) REVERT: A 712 ILE cc_start: 0.7954 (mm) cc_final: 0.7450 (mm) REVERT: A 741 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8394 (tppt) REVERT: A 744 MET cc_start: 0.8871 (mpm) cc_final: 0.8648 (mpp) REVERT: A 908 LEU cc_start: 0.9316 (tp) cc_final: 0.9058 (pp) REVERT: A 925 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8590 (tp30) REVERT: A 970 LEU cc_start: 0.9396 (mt) cc_final: 0.9173 (mp) REVERT: A 1011 GLU cc_start: 0.7973 (tt0) cc_final: 0.7669 (tm-30) REVERT: A 1043 PHE cc_start: 0.9336 (m-80) cc_final: 0.8977 (m-80) REVERT: A 1217 LYS cc_start: 0.9566 (tttt) cc_final: 0.9221 (ttpp) REVERT: A 1238 ILE cc_start: 0.9483 (pt) cc_final: 0.9236 (pt) REVERT: A 1245 MET cc_start: 0.9281 (mtp) cc_final: 0.8893 (mtt) outliers start: 10 outliers final: 3 residues processed: 244 average time/residue: 0.2637 time to fit residues: 85.9429 Evaluate side-chains 158 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1248 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 203 ASN A 703 ASN A 903 HIS ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.147786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.107182 restraints weight = 21353.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.107232 restraints weight = 13541.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.109004 restraints weight = 9291.912| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9774 Z= 0.165 Angle : 0.649 7.324 13244 Z= 0.345 Chirality : 0.043 0.239 1541 Planarity : 0.004 0.046 1644 Dihedral : 6.902 58.469 1332 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.78 % Allowed : 9.40 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.24), residues: 1187 helix: 0.67 (0.18), residues: 760 sheet: 0.51 (0.52), residues: 82 loop : 0.19 (0.37), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 89 HIS 0.006 0.001 HIS A 798 PHE 0.015 0.002 PHE A 714 TYR 0.015 0.002 TYR A 92 ARG 0.010 0.000 ARG A 503 Details of bonding type rmsd hydrogen bonds : bond 0.05312 ( 627) hydrogen bonds : angle 5.39962 ( 1815) covalent geometry : bond 0.00356 ( 9774) covalent geometry : angle 0.64904 (13244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TRP cc_start: 0.5181 (OUTLIER) cc_final: 0.4561 (t-100) REVERT: A 143 PHE cc_start: 0.8099 (m-10) cc_final: 0.7355 (t80) REVERT: A 201 ASP cc_start: 0.8658 (t0) cc_final: 0.8364 (t0) REVERT: A 309 LYS cc_start: 0.8940 (mttp) cc_final: 0.8521 (mtpt) REVERT: A 363 LEU cc_start: 0.8733 (mm) cc_final: 0.8359 (mt) REVERT: A 849 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8373 (mm-40) REVERT: A 873 ILE cc_start: 0.8950 (mm) cc_final: 0.8748 (mt) REVERT: A 890 LYS cc_start: 0.9527 (OUTLIER) cc_final: 0.9300 (mtmm) REVERT: A 911 LEU cc_start: 0.9323 (mt) cc_final: 0.9117 (mt) REVERT: A 915 ARG cc_start: 0.9132 (ptp-110) cc_final: 0.8762 (ptp90) REVERT: A 921 GLU cc_start: 0.8802 (pm20) cc_final: 0.8523 (pm20) REVERT: A 925 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8275 (tp30) REVERT: A 1108 ILE cc_start: 0.8600 (mm) cc_final: 0.8381 (tp) REVERT: A 1131 MET cc_start: 0.9037 (mmm) cc_final: 0.8798 (mmt) REVERT: A 1134 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.7874 (t0) outliers start: 29 outliers final: 13 residues processed: 210 average time/residue: 0.2463 time to fit residues: 72.0175 Evaluate side-chains 154 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1197 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 47 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 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 = 0.4069 r_free = 0.4069 target = 0.147248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.108338 restraints weight = 22051.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107348 restraints weight = 13284.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.108488 restraints weight = 10811.665| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9774 Z= 0.177 Angle : 0.635 10.201 13244 Z= 0.328 Chirality : 0.042 0.349 1541 Planarity : 0.004 0.049 1644 Dihedral : 5.990 54.247 1321 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.74 % Allowed : 12.57 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1187 helix: 1.02 (0.19), residues: 760 sheet: 0.63 (0.52), residues: 81 loop : 0.15 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1147 HIS 0.009 0.001 HIS A1233 PHE 0.038 0.002 PHE A 352 TYR 0.019 0.002 TYR A1259 ARG 0.003 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04844 ( 627) hydrogen bonds : angle 4.99458 ( 1815) covalent geometry : bond 0.00399 ( 9774) covalent geometry : angle 0.63530 (13244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TRP cc_start: 0.5133 (OUTLIER) cc_final: 0.4502 (t-100) REVERT: A 143 PHE cc_start: 0.8258 (m-10) cc_final: 0.7494 (t80) REVERT: A 173 MET cc_start: 0.8836 (ttm) cc_final: 0.8459 (mtt) REVERT: A 201 ASP cc_start: 0.8483 (t0) cc_final: 0.8247 (t0) REVERT: A 210 VAL cc_start: 0.9253 (m) cc_final: 0.9026 (p) REVERT: A 352 PHE cc_start: 0.7915 (m-80) cc_final: 0.7714 (m-80) REVERT: A 357 LEU cc_start: 0.9023 (mt) cc_final: 0.8533 (mp) REVERT: A 849 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8341 (mm-40) REVERT: A 887 ARG cc_start: 0.7232 (ttm170) cc_final: 0.6937 (tpp-160) REVERT: A 1134 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.7838 (t0) outliers start: 39 outliers final: 22 residues processed: 187 average time/residue: 0.2443 time to fit residues: 66.5328 Evaluate side-chains 162 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1134 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 83 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.149008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.109589 restraints weight = 20985.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.110269 restraints weight = 13047.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.110935 restraints weight = 10705.272| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9774 Z= 0.147 Angle : 0.621 12.188 13244 Z= 0.317 Chirality : 0.043 0.410 1541 Planarity : 0.003 0.045 1644 Dihedral : 5.775 57.578 1321 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.74 % Allowed : 15.45 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1187 helix: 1.19 (0.19), residues: 763 sheet: 0.72 (0.52), residues: 83 loop : 0.18 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 89 HIS 0.005 0.001 HIS A1233 PHE 0.030 0.002 PHE A 352 TYR 0.019 0.001 TYR A1259 ARG 0.003 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 627) hydrogen bonds : angle 4.74468 ( 1815) covalent geometry : bond 0.00325 ( 9774) covalent geometry : angle 0.62064 (13244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8160 (tt) REVERT: A 26 TRP cc_start: 0.5016 (OUTLIER) cc_final: 0.4260 (t-100) REVERT: A 143 PHE cc_start: 0.8298 (m-10) cc_final: 0.7494 (t80) REVERT: A 161 CYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7986 (t) REVERT: A 352 PHE cc_start: 0.7931 (m-80) cc_final: 0.7583 (m-80) REVERT: A 849 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8232 (mm-40) REVERT: A 922 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7832 (mmm-85) REVERT: A 1134 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.7745 (t0) REVERT: A 1146 LEU cc_start: 0.8735 (mt) cc_final: 0.8293 (mp) REVERT: A 1166 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7171 (pmm) outliers start: 39 outliers final: 21 residues processed: 181 average time/residue: 0.2185 time to fit residues: 55.7701 Evaluate side-chains 162 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 HIS ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.147191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.107511 restraints weight = 21520.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.108302 restraints weight = 13993.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108290 restraints weight = 9905.770| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9774 Z= 0.149 Angle : 0.603 11.080 13244 Z= 0.311 Chirality : 0.042 0.394 1541 Planarity : 0.003 0.044 1644 Dihedral : 5.647 56.611 1321 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.03 % Allowed : 17.85 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1187 helix: 1.16 (0.18), residues: 772 sheet: 0.91 (0.54), residues: 81 loop : 0.11 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 89 HIS 0.007 0.001 HIS A1037 PHE 0.029 0.002 PHE A 352 TYR 0.020 0.002 TYR A1270 ARG 0.006 0.000 ARG A1132 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 627) hydrogen bonds : angle 4.59323 ( 1815) covalent geometry : bond 0.00335 ( 9774) covalent geometry : angle 0.60324 (13244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8157 (tt) REVERT: A 26 TRP cc_start: 0.5112 (OUTLIER) cc_final: 0.4332 (t-100) REVERT: A 143 PHE cc_start: 0.8394 (m-10) cc_final: 0.7480 (t80) REVERT: A 161 CYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8071 (t) REVERT: A 309 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8416 (ptpt) REVERT: A 352 PHE cc_start: 0.8074 (m-80) cc_final: 0.7744 (m-80) REVERT: A 744 MET cc_start: 0.8511 (mmm) cc_final: 0.8232 (tpp) REVERT: A 849 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8083 (mt0) REVERT: A 915 ARG cc_start: 0.8852 (ptp90) cc_final: 0.8459 (mtt-85) REVERT: A 1006 MET cc_start: 0.8647 (ttm) cc_final: 0.7980 (mtm) REVERT: A 1134 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.7848 (t0) outliers start: 42 outliers final: 26 residues processed: 177 average time/residue: 0.2171 time to fit residues: 55.9174 Evaluate side-chains 165 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1027 TYR Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1268 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.148185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.109334 restraints weight = 22073.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.110188 restraints weight = 14507.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.110669 restraints weight = 11741.203| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9774 Z= 0.163 Angle : 0.631 11.958 13244 Z= 0.319 Chirality : 0.043 0.400 1541 Planarity : 0.003 0.047 1644 Dihedral : 5.664 58.138 1321 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.03 % Allowed : 18.23 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.24), residues: 1187 helix: 1.17 (0.18), residues: 772 sheet: 1.00 (0.54), residues: 81 loop : 0.10 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 89 HIS 0.005 0.001 HIS A 798 PHE 0.029 0.002 PHE A 352 TYR 0.026 0.002 TYR A 289 ARG 0.004 0.000 ARG A1132 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 627) hydrogen bonds : angle 4.57675 ( 1815) covalent geometry : bond 0.00375 ( 9774) covalent geometry : angle 0.63054 (13244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8204 (tt) REVERT: A 26 TRP cc_start: 0.4955 (OUTLIER) cc_final: 0.4210 (t-100) REVERT: A 143 PHE cc_start: 0.8340 (m-10) cc_final: 0.7488 (t80) REVERT: A 161 CYS cc_start: 0.8227 (OUTLIER) cc_final: 0.8025 (t) REVERT: A 170 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7629 (tpp) REVERT: A 238 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7771 (tp) REVERT: A 309 LYS cc_start: 0.8770 (mtmt) cc_final: 0.8261 (ptmt) REVERT: A 352 PHE cc_start: 0.8006 (m-80) cc_final: 0.7800 (m-80) REVERT: A 744 MET cc_start: 0.8429 (mmm) cc_final: 0.8181 (tpp) REVERT: A 849 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8160 (mt0) REVERT: A 915 ARG cc_start: 0.8583 (ptp90) cc_final: 0.8224 (mtt-85) REVERT: A 1134 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.7796 (t0) REVERT: A 1143 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7907 (t70) outliers start: 42 outliers final: 32 residues processed: 176 average time/residue: 0.2040 time to fit residues: 51.8489 Evaluate side-chains 170 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1027 TYR Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1143 ASP Chi-restraints excluded: chain A residue 1268 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS A 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.146130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106815 restraints weight = 22069.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106985 restraints weight = 14545.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.107594 restraints weight = 11750.946| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9774 Z= 0.208 Angle : 0.669 11.200 13244 Z= 0.340 Chirality : 0.044 0.424 1541 Planarity : 0.004 0.045 1644 Dihedral : 5.799 58.895 1321 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.41 % Allowed : 18.62 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1187 helix: 1.05 (0.18), residues: 769 sheet: 0.86 (0.55), residues: 83 loop : 0.02 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 89 HIS 0.006 0.001 HIS A 798 PHE 0.030 0.002 PHE A 352 TYR 0.026 0.002 TYR A 289 ARG 0.005 0.000 ARG A1132 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 627) hydrogen bonds : angle 4.67140 ( 1815) covalent geometry : bond 0.00477 ( 9774) covalent geometry : angle 0.66945 (13244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8313 (tt) REVERT: A 26 TRP cc_start: 0.5031 (OUTLIER) cc_final: 0.4294 (t-100) REVERT: A 143 PHE cc_start: 0.8384 (m-10) cc_final: 0.7547 (t80) REVERT: A 170 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7665 (tpp) REVERT: A 238 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7851 (tp) REVERT: A 309 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8273 (ptmt) REVERT: A 915 ARG cc_start: 0.8650 (ptp90) cc_final: 0.8257 (mtt-85) REVERT: A 1134 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.7874 (t0) REVERT: A 1146 LEU cc_start: 0.8446 (pp) cc_final: 0.8111 (mp) outliers start: 46 outliers final: 32 residues processed: 164 average time/residue: 0.2000 time to fit residues: 48.2882 Evaluate side-chains 163 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1027 TYR Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1268 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 57 optimal weight: 0.0270 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS A 849 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.149784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.110372 restraints weight = 22227.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.110341 restraints weight = 13629.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.111403 restraints weight = 10531.167| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9774 Z= 0.135 Angle : 0.631 12.977 13244 Z= 0.314 Chirality : 0.042 0.410 1541 Planarity : 0.003 0.040 1644 Dihedral : 5.666 59.153 1321 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.55 % Allowed : 19.67 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1187 helix: 1.13 (0.19), residues: 776 sheet: 0.83 (0.55), residues: 83 loop : 0.17 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 89 HIS 0.004 0.001 HIS A 158 PHE 0.026 0.002 PHE A 352 TYR 0.025 0.002 TYR A 289 ARG 0.009 0.000 ARG A1234 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 627) hydrogen bonds : angle 4.48309 ( 1815) covalent geometry : bond 0.00303 ( 9774) covalent geometry : angle 0.63061 (13244) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8139 (tt) REVERT: A 26 TRP cc_start: 0.4986 (OUTLIER) cc_final: 0.4217 (t-100) REVERT: A 177 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8790 (tptt) REVERT: A 238 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7869 (tp) REVERT: A 309 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8309 (ptmt) outliers start: 37 outliers final: 25 residues processed: 161 average time/residue: 0.1958 time to fit residues: 45.7527 Evaluate side-chains 154 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1027 TYR Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 18 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN A 472 HIS A 849 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.147610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.109230 restraints weight = 21915.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.107538 restraints weight = 13928.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.108543 restraints weight = 12617.006| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9774 Z= 0.191 Angle : 0.689 11.844 13244 Z= 0.347 Chirality : 0.044 0.425 1541 Planarity : 0.004 0.040 1644 Dihedral : 5.839 59.958 1321 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.84 % Allowed : 19.48 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.24), residues: 1187 helix: 1.01 (0.18), residues: 776 sheet: 0.85 (0.56), residues: 83 loop : 0.17 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 89 HIS 0.006 0.001 HIS A 158 PHE 0.024 0.002 PHE A 485 TYR 0.025 0.002 TYR A 289 ARG 0.013 0.001 ARG A1234 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 627) hydrogen bonds : angle 4.64839 ( 1815) covalent geometry : bond 0.00441 ( 9774) covalent geometry : angle 0.68887 (13244) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8301 (tt) REVERT: A 26 TRP cc_start: 0.4905 (OUTLIER) cc_final: 0.4190 (t-100) REVERT: A 143 PHE cc_start: 0.8390 (m-10) cc_final: 0.7548 (t80) REVERT: A 177 LYS cc_start: 0.9154 (mmmt) cc_final: 0.8535 (tppt) REVERT: A 238 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7863 (tp) REVERT: A 309 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8268 (ptmt) REVERT: A 920 GLU cc_start: 0.8732 (pp20) cc_final: 0.8055 (pm20) REVERT: A 1113 LEU cc_start: 0.8888 (tp) cc_final: 0.8522 (tt) outliers start: 40 outliers final: 31 residues processed: 154 average time/residue: 0.2016 time to fit residues: 45.0566 Evaluate side-chains 157 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1027 TYR Chi-restraints excluded: chain A residue 1035 TRP Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1117 MET Chi-restraints excluded: chain A residue 1119 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 40 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 903 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.149688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.111654 restraints weight = 22240.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.109810 restraints weight = 13767.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.111065 restraints weight = 12379.655| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9774 Z= 0.144 Angle : 0.667 13.144 13244 Z= 0.332 Chirality : 0.043 0.416 1541 Planarity : 0.003 0.040 1644 Dihedral : 5.771 59.168 1321 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.17 % Allowed : 20.83 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1187 helix: 1.11 (0.19), residues: 776 sheet: 0.93 (0.57), residues: 83 loop : 0.23 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 89 HIS 0.004 0.001 HIS A 158 PHE 0.020 0.002 PHE A 485 TYR 0.030 0.002 TYR A 289 ARG 0.016 0.000 ARG A1234 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 627) hydrogen bonds : angle 4.53042 ( 1815) covalent geometry : bond 0.00324 ( 9774) covalent geometry : angle 0.66725 (13244) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8148 (tt) REVERT: A 26 TRP cc_start: 0.4953 (OUTLIER) cc_final: 0.4191 (t-100) REVERT: A 143 PHE cc_start: 0.8398 (m-10) cc_final: 0.7542 (t80) REVERT: A 177 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8757 (tptt) REVERT: A 238 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7856 (tp) REVERT: A 309 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8261 (ptmt) REVERT: A 1016 TYR cc_start: 0.7886 (m-10) cc_final: 0.7563 (m-10) REVERT: A 1049 MET cc_start: 0.7669 (tpp) cc_final: 0.7384 (tpp) REVERT: A 1146 LEU cc_start: 0.8588 (pp) cc_final: 0.8360 (mp) outliers start: 33 outliers final: 24 residues processed: 156 average time/residue: 0.2003 time to fit residues: 45.1353 Evaluate side-chains 159 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1027 TYR Chi-restraints excluded: chain A residue 1035 TRP Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 75 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 43 optimal weight: 0.0870 chunk 63 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.149960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.112294 restraints weight = 22035.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.111286 restraints weight = 13625.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.112281 restraints weight = 12347.384| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9774 Z= 0.134 Angle : 0.663 13.121 13244 Z= 0.326 Chirality : 0.042 0.411 1541 Planarity : 0.004 0.043 1644 Dihedral : 5.701 58.926 1321 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.98 % Allowed : 20.92 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1187 helix: 1.22 (0.19), residues: 776 sheet: 0.93 (0.57), residues: 83 loop : 0.16 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 89 HIS 0.003 0.001 HIS A 158 PHE 0.022 0.002 PHE A 352 TYR 0.027 0.001 TYR A 289 ARG 0.014 0.001 ARG A1132 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 627) hydrogen bonds : angle 4.46637 ( 1815) covalent geometry : bond 0.00299 ( 9774) covalent geometry : angle 0.66332 (13244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3282.12 seconds wall clock time: 59 minutes 1.00 seconds (3541.00 seconds total)