Starting phenix.real_space_refine on Sat May 24 23:11:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpj_29366/05_2025/8fpj_29366_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpj_29366/05_2025/8fpj_29366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fpj_29366/05_2025/8fpj_29366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpj_29366/05_2025/8fpj_29366.map" model { file = "/net/cci-nas-00/data/ceres_data/8fpj_29366/05_2025/8fpj_29366_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpj_29366/05_2025/8fpj_29366_trim.cif" } resolution = 2.74 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= 0.002 sd= 0.052 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: 6 Type Number sf(0) Gaussians S 70 5.16 5 C 8157 2.51 5 N 2206 2.21 5 O 2383 1.98 5 F 1 1.80 5 H 13143 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25960 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 21983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 21983 Classifications: {'peptide': 1345} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1293} Chain breaks: 2 Chain: "B" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1491 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "C" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 975 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 736 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "E" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 740 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain breaks: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y6L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.44, per 1000 atoms: 0.44 Number of scatterers: 25960 At special positions: 0 Unit cell: (115.92, 102.48, 109.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 70 16.00 F 1 9.00 O 2383 8.00 N 2206 7.00 C 8157 6.00 H 13143 1.00 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: 6.34 Conformation dependent library (CDL) restraints added in 1.8 seconds 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3038 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 9 sheets defined 61.3% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 23 through 36 removed outlier: 3.528A pdb=" N THR A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.638A pdb=" N LYS A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 67 removed outlier: 3.577A pdb=" N LYS A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.687A pdb=" N ASP A 72 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 73 " --> pdb=" O ILE A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 73' Processing helix chain 'A' and resid 77 through 80 Processing helix chain 'A' and resid 81 through 88 Processing helix chain 'A' and resid 93 through 120 removed outlier: 3.584A pdb=" N LEU A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP A 118 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.658A pdb=" N PHE A 138 " --> pdb=" O ASP A 135 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 143 through 167 removed outlier: 3.516A pdb=" N PHE A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 231 Processing helix chain 'A' and resid 243 through 261 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 271 through 285 Processing helix chain 'A' and resid 286 through 316 removed outlier: 3.515A pdb=" N SER A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASN A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 removed outlier: 4.196A pdb=" N ASN A 323 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 347 removed outlier: 3.672A pdb=" N VAL A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.956A pdb=" N PHE A 361 " --> pdb=" O TYR A 358 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 362 " --> pdb=" O TYR A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 362' Processing helix chain 'A' and resid 370 through 380 removed outlier: 3.640A pdb=" N ALA A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N MET A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 376 " --> pdb=" O ARG A 372 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 413 Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 444 through 452 removed outlier: 3.704A pdb=" N PHE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 481 through 488 removed outlier: 3.723A pdb=" N ILE A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TRP A 485 " --> pdb=" O ARG A 482 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER A 486 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A 488 " --> pdb=" O TRP A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.566A pdb=" N PHE A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.616A pdb=" N LYS A 513 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 514 " --> pdb=" O SER A 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 510 through 514' Processing helix chain 'A' and resid 516 through 523 Processing helix chain 'A' and resid 530 through 539 removed outlier: 3.798A pdb=" N SER A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 586 removed outlier: 3.629A pdb=" N ILE A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 595 removed outlier: 3.520A pdb=" N LEU A 594 " --> pdb=" O PHE A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 643 removed outlier: 3.731A pdb=" N ALA A 642 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 660 removed outlier: 4.443A pdb=" N ILE A 650 " --> pdb=" O GLU A 646 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N CYS A 651 " --> pdb=" O THR A 647 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL A 654 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 673 through 675 No H-bonds generated for 'chain 'A' and resid 673 through 675' Processing helix chain 'A' and resid 693 through 697 Processing helix chain 'A' and resid 715 through 734 removed outlier: 3.699A pdb=" N LEU A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 728 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 785 removed outlier: 3.761A pdb=" N ILE A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 806 Processing helix chain 'A' and resid 834 through 847 Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 856 through 874 Processing helix chain 'A' and resid 883 through 901 Processing helix chain 'A' and resid 905 through 913 removed outlier: 4.040A pdb=" N VAL A 909 " --> pdb=" O GLU A 905 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP A 910 " --> pdb=" O ASN A 906 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 911 " --> pdb=" O GLU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 915 No H-bonds generated for 'chain 'A' and resid 914 through 915' Processing helix chain 'A' and resid 916 through 920 Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 937 through 953 Processing helix chain 'A' and resid 957 through 970 removed outlier: 3.545A pdb=" N LYS A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 962 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE A 965 " --> pdb=" O LYS A 961 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 966 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 985 Processing helix chain 'A' and resid 997 through 1012 removed outlier: 3.632A pdb=" N ILE A1001 " --> pdb=" O VAL A 997 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR A1004 " --> pdb=" O ASP A1000 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA A1005 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A1012 " --> pdb=" O SER A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1033 removed outlier: 4.629A pdb=" N SER A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ARG A1027 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A1033 " --> pdb=" O GLU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1053 Processing helix chain 'A' and resid 1055 through 1068 removed outlier: 3.849A pdb=" N GLY A1068 " --> pdb=" O ASN A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1097 Processing helix chain 'A' and resid 1099 through 1105 Processing helix chain 'A' and resid 1123 through 1135 Processing helix chain 'A' and resid 1207 through 1224 Processing helix chain 'A' and resid 1229 through 1242 Processing helix chain 'A' and resid 1245 through 1250 Processing helix chain 'A' and resid 1251 through 1253 No H-bonds generated for 'chain 'A' and resid 1251 through 1253' Processing helix chain 'A' and resid 1260 through 1265 Processing helix chain 'A' and resid 1279 through 1284 Processing helix chain 'A' and resid 1290 through 1301 Processing helix chain 'A' and resid 1309 through 1328 removed outlier: 3.505A pdb=" N GLU A1325 " --> pdb=" O MET A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1344 Processing helix chain 'A' and resid 1358 through 1368 removed outlier: 4.417A pdb=" N ASP A1362 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS A1363 " --> pdb=" O LYS A1359 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1372 Processing helix chain 'B' and resid 173 through 193 Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 228 through 239 removed outlier: 3.610A pdb=" N GLU B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 removed outlier: 4.114A pdb=" N LEU B 258 " --> pdb=" O LYS B 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 198 removed outlier: 3.681A pdb=" N ALA C 198 " --> pdb=" O ASN C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.594A pdb=" N ASP C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'D' and resid 173 through 193 removed outlier: 3.758A pdb=" N THR D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 205 through 218 removed outlier: 4.195A pdb=" N ASP D 209 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA D 210 " --> pdb=" O GLY D 206 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG D 215 " --> pdb=" O MET D 211 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLU D 216 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D 218 " --> pdb=" O ILE D 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 191 removed outlier: 3.720A pdb=" N SER E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 226 removed outlier: 3.637A pdb=" N GLU E 217 " --> pdb=" O GLY E 213 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA E 220 " --> pdb=" O GLU E 216 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 removed outlier: 6.043A pdb=" N LYS A 74 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N PHE A 200 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 389 Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AA5, first strand: chain 'A' and resid 737 through 743 Processing sheet with id=AA6, first strand: chain 'A' and resid 807 through 809 removed outlier: 4.305A pdb=" N ILE A 807 " --> pdb=" O HIS A 814 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1153 through 1157 Processing sheet with id=AA8, first strand: chain 'A' and resid 1196 through 1197 Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 200 656 hydrogen bonds defined for protein. 1854 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: 9.88 Time building geometry restraints manager: 7.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13122 1.03 - 1.23: 31 1.23 - 1.42: 5213 1.42 - 1.62: 7684 1.62 - 1.81: 119 Bond restraints: 26169 Sorted by residual: bond pdb=" O Y6L A9901 " pdb=" C19 Y6L A9901 " ideal model delta sigma weight residual 1.412 1.452 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C20 Y6L A9901 " pdb=" C21 Y6L A9901 " ideal model delta sigma weight residual 1.514 1.485 0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C ALA A 954 " pdb=" N ASN A 955 " ideal model delta sigma weight residual 1.332 1.313 0.019 1.40e-02 5.10e+03 1.87e+00 bond pdb=" C14 Y6L A9901 " pdb=" N3 Y6L A9901 " ideal model delta sigma weight residual 1.369 1.345 0.024 2.00e-02 2.50e+03 1.48e+00 bond pdb=" CB ASN A1312 " pdb=" CG ASN A1312 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.34e+00 ... (remaining 26164 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 44985 1.20 - 2.39: 2326 2.39 - 3.59: 130 3.59 - 4.79: 28 4.79 - 5.99: 3 Bond angle restraints: 47472 Sorted by residual: angle pdb=" N VAL A 423 " pdb=" CA VAL A 423 " pdb=" C VAL A 423 " ideal model delta sigma weight residual 112.29 108.65 3.64 9.40e-01 1.13e+00 1.50e+01 angle pdb=" N ILE A 818 " pdb=" CA ILE A 818 " pdb=" C ILE A 818 " ideal model delta sigma weight residual 106.21 109.96 -3.75 1.07e+00 8.73e-01 1.23e+01 angle pdb=" N HIS A 90 " pdb=" CA HIS A 90 " pdb=" C HIS A 90 " ideal model delta sigma weight residual 109.65 105.17 4.48 1.56e+00 4.11e-01 8.25e+00 angle pdb=" C VAL A1155 " pdb=" N ILE A1156 " pdb=" CA ILE A1156 " ideal model delta sigma weight residual 123.46 120.40 3.06 1.37e+00 5.33e-01 4.97e+00 angle pdb=" N LYS A 19 " pdb=" CA LYS A 19 " pdb=" CB LYS A 19 " ideal model delta sigma weight residual 112.78 109.51 3.27 1.53e+00 4.27e-01 4.57e+00 ... (remaining 47467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 11028 17.52 - 35.04: 837 35.04 - 52.55: 191 52.55 - 70.07: 66 70.07 - 87.59: 15 Dihedral angle restraints: 12137 sinusoidal: 6825 harmonic: 5312 Sorted by residual: dihedral pdb=" CA ARG A 362 " pdb=" C ARG A 362 " pdb=" N ILE A 363 " pdb=" CA ILE A 363 " ideal model delta harmonic sigma weight residual -180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA CYS A 261 " pdb=" C CYS A 261 " pdb=" N CYS A 262 " pdb=" CA CYS A 262 " ideal model delta harmonic sigma weight residual 180.00 -157.08 -22.92 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA ASN A 204 " pdb=" C ASN A 204 " pdb=" N GLN A 205 " pdb=" CA GLN A 205 " ideal model delta harmonic sigma weight residual -180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 12134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1235 0.028 - 0.057: 537 0.057 - 0.085: 147 0.085 - 0.113: 69 0.113 - 0.142: 33 Chirality restraints: 2021 Sorted by residual: chirality pdb=" CA VAL A1267 " pdb=" N VAL A1267 " pdb=" C VAL A1267 " pdb=" CB VAL A1267 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE A1039 " pdb=" N ILE A1039 " pdb=" C ILE A1039 " pdb=" CB ILE A1039 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE A 915 " pdb=" N ILE A 915 " pdb=" C ILE A 915 " pdb=" CB ILE A 915 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 2018 not shown) Planarity restraints: 3753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 Y6L A9901 " 0.034 2.00e-02 2.50e+03 7.06e-02 6.22e+01 pdb=" C15 Y6L A9901 " -0.067 2.00e-02 2.50e+03 pdb=" N2 Y6L A9901 " -0.088 2.00e-02 2.50e+03 pdb=" N3 Y6L A9901 " 0.106 2.00e-02 2.50e+03 pdb=" O2 Y6L A9901 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 Y6L A9901 " -0.037 2.00e-02 2.50e+03 3.91e-02 1.91e+01 pdb=" C13 Y6L A9901 " 0.018 2.00e-02 2.50e+03 pdb=" N2 Y6L A9901 " 0.060 2.00e-02 2.50e+03 pdb=" N3 Y6L A9901 " -0.048 2.00e-02 2.50e+03 pdb=" O3 Y6L A9901 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 415 " 0.011 2.00e-02 2.50e+03 1.10e-02 4.82e+00 pdb=" CG TRP A 415 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 415 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 415 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 415 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 415 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 415 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 415 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 415 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 415 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 415 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP A 415 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 415 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 415 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 415 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 415 " -0.000 2.00e-02 2.50e+03 ... (remaining 3750 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 927 2.18 - 2.78: 52078 2.78 - 3.39: 71087 3.39 - 3.99: 92647 3.99 - 4.60: 146719 Nonbonded interactions: 363458 Sorted by model distance: nonbonded pdb=" OD1 ASP A 653 " pdb="HH22 ARG C 215 " model vdw 1.570 2.450 nonbonded pdb=" OE2 GLU A1060 " pdb="HD21 ASN A1064 " model vdw 1.611 2.450 nonbonded pdb="HD22 ASN A 88 " pdb=" O LEU A 176 " model vdw 1.616 2.450 nonbonded pdb="HH22 ARG A 341 " pdb=" O GLU B 265 " model vdw 1.634 2.450 nonbonded pdb=" H LYS A1117 " pdb=" O ARG A1121 " model vdw 1.636 2.450 ... (remaining 363453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.49 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.470 Extract box with map and model: 1.050 Check model and map are aligned: 0.100 Set scattering table: 0.240 Process input model: 52.080 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 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:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 : 0.003 0.040 13026 Z= 0.153 Angle : 0.573 5.987 17566 Z= 0.322 Chirality : 0.039 0.142 2021 Planarity : 0.004 0.071 2220 Dihedral : 13.899 87.590 5007 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.21), residues: 1578 helix: 0.89 (0.18), residues: 835 sheet: -0.15 (0.63), residues: 72 loop : -1.53 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 415 HIS 0.012 0.002 HIS A 286 PHE 0.013 0.001 PHE A1310 TYR 0.014 0.001 TYR A 706 ARG 0.004 0.000 ARG A 341 Details of bonding type rmsd hydrogen bonds : bond 0.17082 ( 656) hydrogen bonds : angle 6.03423 ( 1854) covalent geometry : bond 0.00340 (13026) covalent geometry : angle 0.57349 (17566) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.8425 (ttp) cc_final: 0.8153 (ttm) REVERT: A 910 ASP cc_start: 0.7515 (m-30) cc_final: 0.7302 (m-30) REVERT: A 1096 GLU cc_start: 0.7376 (tt0) cc_final: 0.7059 (tp30) REVERT: A 1307 ASN cc_start: 0.7372 (m110) cc_final: 0.7164 (m-40) REVERT: A 1340 GLN cc_start: 0.7205 (mt0) cc_final: 0.6709 (mm110) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 2.9890 time to fit residues: 659.2129 Evaluate side-chains 155 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 743 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN B 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.158010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124116 restraints weight = 39103.221| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.91 r_work: 0.3328 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13026 Z= 0.148 Angle : 0.551 6.023 17566 Z= 0.299 Chirality : 0.039 0.144 2021 Planarity : 0.004 0.048 2220 Dihedral : 4.950 25.352 1751 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.11 % Allowed : 8.08 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.02 (0.21), residues: 1578 helix: 1.09 (0.18), residues: 860 sheet: -0.13 (0.61), residues: 72 loop : -1.46 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 142 HIS 0.011 0.001 HIS A 286 PHE 0.013 0.001 PHE A1310 TYR 0.015 0.001 TYR A 706 ARG 0.005 0.000 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.05867 ( 656) hydrogen bonds : angle 4.52201 ( 1854) covalent geometry : bond 0.00337 (13026) covalent geometry : angle 0.55054 (17566) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 1.826 Fit side-chains revert: symmetry clash REVERT: A 257 MET cc_start: 0.8647 (ttp) cc_final: 0.8367 (ttm) REVERT: A 440 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: A 503 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: A 790 LYS cc_start: 0.8233 (mttp) cc_final: 0.7441 (mtpp) REVERT: A 1096 GLU cc_start: 0.8135 (tt0) cc_final: 0.7733 (tp30) REVERT: A 1247 LYS cc_start: 0.7948 (pttt) cc_final: 0.7379 (pptt) REVERT: A 1340 GLN cc_start: 0.7530 (mt0) cc_final: 0.6768 (mm110) REVERT: A 1345 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6864 (m-30) REVERT: B 250 LYS cc_start: 0.8215 (tttm) cc_final: 0.7474 (tptt) outliers start: 16 outliers final: 4 residues processed: 169 average time/residue: 2.7659 time to fit residues: 510.3130 Evaluate side-chains 155 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1345 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 743 ASN A1028 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN A1353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.155322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121119 restraints weight = 38858.652| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.93 r_work: 0.3292 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13026 Z= 0.172 Angle : 0.567 6.046 17566 Z= 0.306 Chirality : 0.040 0.149 2021 Planarity : 0.004 0.048 2220 Dihedral : 4.971 24.907 1751 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.46 % Allowed : 9.48 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.07 (0.21), residues: 1578 helix: 1.16 (0.18), residues: 861 sheet: -0.21 (0.59), residues: 72 loop : -1.49 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 415 HIS 0.011 0.001 HIS A 286 PHE 0.015 0.002 PHE A1310 TYR 0.016 0.002 TYR A 706 ARG 0.006 0.000 ARG A 852 Details of bonding type rmsd hydrogen bonds : bond 0.06066 ( 656) hydrogen bonds : angle 4.36545 ( 1854) covalent geometry : bond 0.00413 (13026) covalent geometry : angle 0.56664 (17566) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 2.008 Fit side-chains revert: symmetry clash REVERT: A 257 MET cc_start: 0.8679 (ttp) cc_final: 0.8399 (ttm) REVERT: A 282 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7776 (ttm170) REVERT: A 440 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7061 (tm-30) REVERT: A 503 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: A 691 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7659 (pp20) REVERT: A 790 LYS cc_start: 0.8266 (mttp) cc_final: 0.7476 (mtpp) REVERT: A 905 GLU cc_start: 0.7472 (tp30) cc_final: 0.7198 (tp30) REVERT: A 1096 GLU cc_start: 0.8195 (tt0) cc_final: 0.7789 (tp30) REVERT: A 1247 LYS cc_start: 0.8056 (pttt) cc_final: 0.7460 (pptt) REVERT: A 1333 LYS cc_start: 0.8109 (tptt) cc_final: 0.7837 (tptt) REVERT: A 1340 GLN cc_start: 0.7708 (mt0) cc_final: 0.6988 (mm110) REVERT: A 1345 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.7000 (m-30) REVERT: B 250 LYS cc_start: 0.8277 (tttm) cc_final: 0.7531 (tptt) outliers start: 21 outliers final: 7 residues processed: 165 average time/residue: 2.9771 time to fit residues: 538.9962 Evaluate side-chains 159 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1345 ASP Chi-restraints excluded: chain A residue 1362 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN B 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.157830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123871 restraints weight = 39304.229| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.93 r_work: 0.3314 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13026 Z= 0.117 Angle : 0.507 5.884 17566 Z= 0.272 Chirality : 0.038 0.139 2021 Planarity : 0.004 0.046 2220 Dihedral : 4.747 23.269 1751 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.88 % Allowed : 10.31 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1578 helix: 1.32 (0.18), residues: 867 sheet: -0.16 (0.58), residues: 72 loop : -1.46 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 142 HIS 0.008 0.001 HIS A 286 PHE 0.014 0.001 PHE A1310 TYR 0.011 0.001 TYR A 706 ARG 0.005 0.000 ARG A 852 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 656) hydrogen bonds : angle 4.19064 ( 1854) covalent geometry : bond 0.00266 (13026) covalent geometry : angle 0.50706 (17566) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.8638 (ttp) cc_final: 0.8395 (ttm) REVERT: A 282 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7747 (ttm170) REVERT: A 373 ASP cc_start: 0.8053 (t0) cc_final: 0.7662 (t0) REVERT: A 375 MET cc_start: 0.8425 (mtp) cc_final: 0.8000 (mtp) REVERT: A 440 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7065 (tm-30) REVERT: A 503 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: A 790 LYS cc_start: 0.8271 (mttp) cc_final: 0.7479 (mtpp) REVERT: A 905 GLU cc_start: 0.7492 (tp30) cc_final: 0.7224 (tp30) REVERT: A 1096 GLU cc_start: 0.8185 (tt0) cc_final: 0.7754 (tp30) REVERT: A 1247 LYS cc_start: 0.8016 (pttt) cc_final: 0.7462 (pptt) REVERT: A 1310 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7199 (t80) REVERT: A 1340 GLN cc_start: 0.7735 (mt0) cc_final: 0.7131 (mm110) REVERT: B 250 LYS cc_start: 0.8240 (tttm) cc_final: 0.7494 (tptt) REVERT: C 211 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7229 (mtt) outliers start: 27 outliers final: 8 residues processed: 171 average time/residue: 2.8618 time to fit residues: 534.1346 Evaluate side-chains 164 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1310 PHE Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain C residue 211 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 114 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 0.0370 chunk 62 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 154 optimal weight: 0.0170 chunk 69 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 525 ASN A 743 ASN A 955 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN A1353 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.156368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124588 restraints weight = 40982.962| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.85 r_work: 0.3351 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13026 Z= 0.142 Angle : 0.532 5.816 17566 Z= 0.285 Chirality : 0.039 0.145 2021 Planarity : 0.004 0.050 2220 Dihedral : 4.776 23.457 1751 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.81 % Allowed : 11.50 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.23 (0.21), residues: 1578 helix: 1.31 (0.18), residues: 867 sheet: -0.17 (0.58), residues: 72 loop : -1.45 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 142 HIS 0.007 0.001 HIS A 286 PHE 0.014 0.001 PHE A1310 TYR 0.014 0.001 TYR A 706 ARG 0.006 0.000 ARG A 852 Details of bonding type rmsd hydrogen bonds : bond 0.05348 ( 656) hydrogen bonds : angle 4.16085 ( 1854) covalent geometry : bond 0.00337 (13026) covalent geometry : angle 0.53216 (17566) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.8692 (ttp) cc_final: 0.8433 (ttm) REVERT: A 282 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7799 (ttm170) REVERT: A 341 ARG cc_start: 0.8029 (mmm-85) cc_final: 0.7711 (mtp180) REVERT: A 375 MET cc_start: 0.8496 (mtp) cc_final: 0.8256 (mtp) REVERT: A 440 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7081 (tm-30) REVERT: A 503 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7263 (tt0) REVERT: A 790 LYS cc_start: 0.8335 (mttp) cc_final: 0.7572 (mtpp) REVERT: A 905 GLU cc_start: 0.7456 (tp30) cc_final: 0.7070 (tp30) REVERT: A 1096 GLU cc_start: 0.8144 (tt0) cc_final: 0.7771 (tp30) REVERT: A 1247 LYS cc_start: 0.8163 (pttt) cc_final: 0.7611 (pptt) REVERT: A 1340 GLN cc_start: 0.7890 (mt0) cc_final: 0.7299 (mm110) REVERT: A 1345 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.7162 (m-30) outliers start: 26 outliers final: 14 residues processed: 175 average time/residue: 2.8712 time to fit residues: 549.3497 Evaluate side-chains 166 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1345 ASP Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 194 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 46 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 525 ASN A 743 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120942 restraints weight = 41188.898| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.87 r_work: 0.3304 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13026 Z= 0.193 Angle : 0.592 5.659 17566 Z= 0.319 Chirality : 0.041 0.152 2021 Planarity : 0.005 0.057 2220 Dihedral : 5.024 25.540 1751 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.02 % Allowed : 12.06 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.03 (0.21), residues: 1578 helix: 1.14 (0.18), residues: 861 sheet: -0.25 (0.53), residues: 84 loop : -1.54 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 142 HIS 0.013 0.002 HIS A 945 PHE 0.015 0.002 PHE A1310 TYR 0.017 0.002 TYR A 706 ARG 0.007 0.001 ARG A 852 Details of bonding type rmsd hydrogen bonds : bond 0.06294 ( 656) hydrogen bonds : angle 4.24411 ( 1854) covalent geometry : bond 0.00470 (13026) covalent geometry : angle 0.59214 (17566) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.8718 (ttp) cc_final: 0.8454 (ttm) REVERT: A 282 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7814 (ttm170) REVERT: A 341 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.7688 (mtp180) REVERT: A 440 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7027 (tm-30) REVERT: A 503 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7293 (tt0) REVERT: A 790 LYS cc_start: 0.8409 (mttp) cc_final: 0.7652 (mtpp) REVERT: A 791 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6755 (mm-30) REVERT: A 905 GLU cc_start: 0.7470 (tp30) cc_final: 0.7024 (tp30) REVERT: A 1096 GLU cc_start: 0.8140 (tt0) cc_final: 0.7750 (tp30) REVERT: A 1247 LYS cc_start: 0.8236 (pttt) cc_final: 0.7658 (pptt) REVERT: A 1340 GLN cc_start: 0.7872 (mt0) cc_final: 0.7415 (mm110) outliers start: 29 outliers final: 13 residues processed: 173 average time/residue: 2.7660 time to fit residues: 523.3152 Evaluate side-chains 167 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 194 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 99 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 743 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.153603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121714 restraints weight = 41195.351| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.85 r_work: 0.3312 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13026 Z= 0.166 Angle : 0.565 5.916 17566 Z= 0.303 Chirality : 0.040 0.146 2021 Planarity : 0.004 0.058 2220 Dihedral : 4.967 25.336 1751 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.81 % Allowed : 13.45 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.06 (0.21), residues: 1578 helix: 1.17 (0.18), residues: 864 sheet: -0.27 (0.59), residues: 73 loop : -1.52 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 142 HIS 0.009 0.001 HIS A 945 PHE 0.013 0.002 PHE A1310 TYR 0.015 0.002 TYR A 706 ARG 0.008 0.000 ARG A 852 Details of bonding type rmsd hydrogen bonds : bond 0.05817 ( 656) hydrogen bonds : angle 4.14841 ( 1854) covalent geometry : bond 0.00399 (13026) covalent geometry : angle 0.56489 (17566) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.8697 (ttp) cc_final: 0.8461 (ttm) REVERT: A 282 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7802 (ttm170) REVERT: A 341 ARG cc_start: 0.8034 (mmm-85) cc_final: 0.7673 (mtp180) REVERT: A 440 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7111 (tm-30) REVERT: A 503 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: A 677 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8694 (mmm) REVERT: A 790 LYS cc_start: 0.8403 (mttp) cc_final: 0.7659 (mtpp) REVERT: A 791 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6805 (mm-30) REVERT: A 905 GLU cc_start: 0.7438 (tp30) cc_final: 0.6990 (tp30) REVERT: A 1096 GLU cc_start: 0.8151 (tt0) cc_final: 0.7738 (tp30) REVERT: A 1247 LYS cc_start: 0.8247 (pttt) cc_final: 0.7664 (pptt) REVERT: A 1340 GLN cc_start: 0.7813 (mt0) cc_final: 0.7417 (mm-40) REVERT: A 1345 ASP cc_start: 0.7575 (m-30) cc_final: 0.7021 (m-30) outliers start: 26 outliers final: 14 residues processed: 173 average time/residue: 2.7557 time to fit residues: 522.8626 Evaluate side-chains 172 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 194 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 152 optimal weight: 9.9990 chunk 30 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 525 ASN A 743 ASN ** A1162 HIS ** 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 = 0.3790 r_free = 0.3790 target = 0.155089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123478 restraints weight = 40967.489| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.84 r_work: 0.3337 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13026 Z= 0.131 Angle : 0.531 5.695 17566 Z= 0.284 Chirality : 0.038 0.140 2021 Planarity : 0.004 0.060 2220 Dihedral : 4.817 24.091 1751 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.46 % Allowed : 13.94 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.21 (0.21), residues: 1578 helix: 1.29 (0.18), residues: 867 sheet: -0.28 (0.59), residues: 73 loop : -1.46 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 142 HIS 0.006 0.001 HIS A 945 PHE 0.013 0.001 PHE A1310 TYR 0.013 0.001 TYR A 706 ARG 0.009 0.000 ARG A 852 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 656) hydrogen bonds : angle 4.05145 ( 1854) covalent geometry : bond 0.00308 (13026) covalent geometry : angle 0.53075 (17566) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.8679 (ttp) cc_final: 0.8452 (ttm) REVERT: A 341 ARG cc_start: 0.8019 (mmm-85) cc_final: 0.7648 (mtp180) REVERT: A 380 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8300 (tt) REVERT: A 440 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: A 503 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: A 677 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8603 (mmm) REVERT: A 790 LYS cc_start: 0.8395 (mttp) cc_final: 0.7656 (mtpp) REVERT: A 806 VAL cc_start: 0.7992 (p) cc_final: 0.7740 (t) REVERT: A 905 GLU cc_start: 0.7414 (tp30) cc_final: 0.6976 (tp30) REVERT: A 1096 GLU cc_start: 0.8147 (tt0) cc_final: 0.7724 (tp30) REVERT: A 1247 LYS cc_start: 0.8190 (pttt) cc_final: 0.7615 (pptt) REVERT: A 1340 GLN cc_start: 0.7798 (mt0) cc_final: 0.7391 (mm110) outliers start: 21 outliers final: 11 residues processed: 170 average time/residue: 2.8264 time to fit residues: 523.3333 Evaluate side-chains 168 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 194 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 25 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 743 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121221 restraints weight = 41132.714| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.84 r_work: 0.3306 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13026 Z= 0.178 Angle : 0.578 5.836 17566 Z= 0.311 Chirality : 0.040 0.148 2021 Planarity : 0.004 0.067 2220 Dihedral : 4.961 25.078 1751 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.53 % Allowed : 14.56 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.06 (0.21), residues: 1578 helix: 1.18 (0.18), residues: 864 sheet: -0.33 (0.58), residues: 73 loop : -1.52 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 142 HIS 0.008 0.001 HIS A 683 PHE 0.015 0.002 PHE A1310 TYR 0.015 0.002 TYR A 706 ARG 0.009 0.000 ARG A 852 Details of bonding type rmsd hydrogen bonds : bond 0.05980 ( 656) hydrogen bonds : angle 4.12429 ( 1854) covalent geometry : bond 0.00432 (13026) covalent geometry : angle 0.57823 (17566) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.8718 (ttp) cc_final: 0.8473 (ttm) REVERT: A 341 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7687 (mtp180) REVERT: A 380 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8272 (tt) REVERT: A 440 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: A 503 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7300 (tt0) REVERT: A 677 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8664 (mmm) REVERT: A 790 LYS cc_start: 0.8433 (mttp) cc_final: 0.7712 (mtpp) REVERT: A 806 VAL cc_start: 0.8014 (p) cc_final: 0.7773 (t) REVERT: A 905 GLU cc_start: 0.7442 (tp30) cc_final: 0.6991 (tp30) REVERT: A 1096 GLU cc_start: 0.8165 (tt0) cc_final: 0.7749 (tp30) REVERT: A 1247 LYS cc_start: 0.8244 (pttt) cc_final: 0.7909 (tttm) REVERT: A 1340 GLN cc_start: 0.7773 (mt0) cc_final: 0.7471 (mm110) REVERT: A 1345 ASP cc_start: 0.7604 (m-30) cc_final: 0.7054 (m-30) REVERT: C 233 MET cc_start: 0.3642 (ppp) cc_final: 0.2494 (pmt) outliers start: 22 outliers final: 15 residues processed: 171 average time/residue: 2.7704 time to fit residues: 517.1717 Evaluate side-chains 173 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain C residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 743 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.154639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122526 restraints weight = 41046.735| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.87 r_work: 0.3323 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13026 Z= 0.161 Angle : 0.561 5.758 17566 Z= 0.301 Chirality : 0.040 0.142 2021 Planarity : 0.004 0.070 2220 Dihedral : 4.934 25.240 1751 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.39 % Allowed : 14.84 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.10 (0.21), residues: 1578 helix: 1.21 (0.18), residues: 864 sheet: -0.31 (0.58), residues: 73 loop : -1.51 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 142 HIS 0.006 0.001 HIS A 945 PHE 0.014 0.002 PHE A1310 TYR 0.015 0.002 TYR A 706 ARG 0.009 0.000 ARG A 852 Details of bonding type rmsd hydrogen bonds : bond 0.05717 ( 656) hydrogen bonds : angle 4.09988 ( 1854) covalent geometry : bond 0.00388 (13026) covalent geometry : angle 0.56080 (17566) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.8704 (ttp) cc_final: 0.8475 (ttm) REVERT: A 341 ARG cc_start: 0.8045 (mmm-85) cc_final: 0.7658 (mtp180) REVERT: A 380 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8225 (tt) REVERT: A 440 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: A 503 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: A 677 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8613 (mmm) REVERT: A 790 LYS cc_start: 0.8436 (mttp) cc_final: 0.7702 (mtpp) REVERT: A 791 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6820 (mm-30) REVERT: A 806 VAL cc_start: 0.7970 (p) cc_final: 0.7730 (t) REVERT: A 905 GLU cc_start: 0.7429 (tp30) cc_final: 0.6965 (tp30) REVERT: A 1096 GLU cc_start: 0.8160 (tt0) cc_final: 0.7733 (tp30) REVERT: A 1247 LYS cc_start: 0.8236 (pttt) cc_final: 0.7896 (tttm) REVERT: A 1340 GLN cc_start: 0.7759 (mt0) cc_final: 0.7490 (mm110) REVERT: A 1345 ASP cc_start: 0.7591 (m-30) cc_final: 0.7068 (m-30) REVERT: C 233 MET cc_start: 0.3626 (ppp) cc_final: 0.2612 (pmt) outliers start: 20 outliers final: 14 residues processed: 171 average time/residue: 2.7897 time to fit residues: 524.2067 Evaluate side-chains 176 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain C residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 35 optimal weight: 0.0870 chunk 104 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 138 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 98 optimal weight: 0.0870 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 525 ASN A 743 ASN ** A1162 HIS ** 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 = 0.3822 r_free = 0.3822 target = 0.158047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126791 restraints weight = 41034.761| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.84 r_work: 0.3382 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 13026 Z= 0.101 Angle : 0.493 5.467 17566 Z= 0.263 Chirality : 0.037 0.139 2021 Planarity : 0.004 0.064 2220 Dihedral : 4.604 23.822 1751 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.84 % Allowed : 15.61 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.44 (0.22), residues: 1578 helix: 1.49 (0.18), residues: 866 sheet: -0.18 (0.59), residues: 73 loop : -1.37 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 142 HIS 0.007 0.001 HIS A 286 PHE 0.012 0.001 PHE A1310 TYR 0.012 0.001 TYR A 645 ARG 0.009 0.000 ARG A 852 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 656) hydrogen bonds : angle 3.93267 ( 1854) covalent geometry : bond 0.00224 (13026) covalent geometry : angle 0.49259 (17566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15118.28 seconds wall clock time: 259 minutes 7.70 seconds (15547.70 seconds total)