Starting phenix.real_space_refine on Thu Aug 6 04:41:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ye6_39190/08_2026/8ye6_39190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ye6_39190/08_2026/8ye6_39190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ye6_39190/08_2026/8ye6_39190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ye6_39190/08_2026/8ye6_39190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ye6_39190/08_2026/8ye6_39190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ye6_39190/08_2026/8ye6_39190.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.135 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: 5 Type Number sf(0) Gaussians P 92 5.49 5 S 26 5.16 5 C 8275 2.51 5 N 2378 2.21 5 O 2832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13603 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 727 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} Chain: "A" Number of atoms: 10903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1359, 10903 Classifications: {'peptide': 1359} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 35, 'TRANS': 1323} Chain breaks: 3 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "C" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1973 Classifications: {'RNA': 92} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 46, 'rna3p_pyr': 32} Link IDs: {'rna2p': 14, 'rna3p': 77} Time building chain proxies: 3.64, per 1000 atoms: 0.27 Number of scatterers: 13603 At special positions: 0 Unit cell: (91.5705, 118.503, 128.199, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 92 15.00 O 2832 8.00 N 2378 7.00 C 8275 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: 1.03 Conformation dependent library (CDL) restraints added in 725.8 milliseconds 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2758 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 11 sheets defined 52.7% alpha, 7.5% beta 17 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 24 through 34 Processing helix chain 'B' and resid 46 through 68 removed outlier: 3.923A pdb=" N LYS B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 92 removed outlier: 3.992A pdb=" N LYS B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 94 removed outlier: 5.198A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.516A pdb=" N GLU A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 removed outlier: 4.000A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.820A pdb=" N ASP A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.951A pdb=" N PHE A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 286 through 306 removed outlier: 3.857A pdb=" N LYS A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.671A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 removed outlier: 3.749A pdb=" N PHE A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Proline residue: A 378 - end of helix removed outlier: 3.523A pdb=" N LYS A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.598A pdb=" N LEU A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.615A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 410' Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.194A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.901A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.977A pdb=" N LEU A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 608 removed outlier: 3.622A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.716A pdb=" N LEU A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 637 through 638 No H-bonds generated for 'chain 'A' and resid 637 through 638' Processing helix chain 'A' and resid 639 through 643 Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 719 through 727 removed outlier: 3.682A pdb=" N LEU A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 Processing helix chain 'A' and resid 775 through 792 removed outlier: 3.920A pdb=" N GLU A 779 " --> pdb=" O LYS A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 removed outlier: 3.984A pdb=" N GLU A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 832 through 836 removed outlier: 3.673A pdb=" N TYR A 836 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 removed outlier: 4.131A pdb=" N ARG A 864 " --> pdb=" O ASP A 861 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A 865 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 879 Processing helix chain 'A' and resid 879 through 889 Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 909 through 922 removed outlier: 3.944A pdb=" N VAL A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 940 Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 981 through 1001 removed outlier: 3.582A pdb=" N ALA A 987 " --> pdb=" O HIS A 983 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 995 " --> pdb=" O ALA A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1087 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.586A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1184 Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.600A pdb=" N LEU A1194 " --> pdb=" O LYS A1191 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1191 through 1195' Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1261 Processing helix chain 'A' and resid 1264 through 1280 Processing helix chain 'A' and resid 1283 through 1296 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 4.091A pdb=" N GLU A1307 " --> pdb=" O ARG A1303 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.568A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 removed outlier: 3.513A pdb=" N ILE A 21 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE A 48 " --> pdb=" O ASN A1093 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL A1095 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA A 50 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.172A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 509 removed outlier: 5.260A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 530 Processing sheet with id=AA5, first strand: chain 'A' and resid 758 through 761 Processing sheet with id=AA6, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA7, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA8, first strand: chain 'A' and resid 1063 through 1065 Processing sheet with id=AA9, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB1, first strand: chain 'A' and resid 1157 through 1167 removed outlier: 5.831A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1324 through 1325 507 hydrogen bonds defined for protein. 1488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 1.47 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: 2570 1.32 - 1.45: 3897 1.45 - 1.57: 7351 1.57 - 1.70: 176 1.70 - 1.83: 49 Bond restraints: 14043 Sorted by residual: bond pdb=" N9 A C 49 " pdb=" C4 A C 49 " ideal model delta sigma weight residual 1.374 1.341 0.033 6.00e-03 2.78e+04 3.05e+01 bond pdb=" C2 U C 24 " pdb=" N3 U C 24 " ideal model delta sigma weight residual 1.373 1.340 0.033 7.00e-03 2.04e+04 2.16e+01 bond pdb=" N3 U C 24 " pdb=" C4 U C 24 " ideal model delta sigma weight residual 1.380 1.338 0.042 9.00e-03 1.23e+04 2.16e+01 bond pdb=" N9 A C 47 " pdb=" C4 A C 47 " ideal model delta sigma weight residual 1.374 1.347 0.027 6.00e-03 2.78e+04 1.99e+01 bond pdb=" C5 G C 27 " pdb=" C4 G C 27 " ideal model delta sigma weight residual 1.379 1.348 0.031 7.00e-03 2.04e+04 1.95e+01 ... (remaining 14038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 18997 3.28 - 6.56: 348 6.56 - 9.84: 33 9.84 - 13.13: 4 13.13 - 16.41: 1 Bond angle restraints: 19383 Sorted by residual: angle pdb=" O2 U C 24 " pdb=" C2 U C 24 " pdb=" N3 U C 24 " ideal model delta sigma weight residual 122.20 113.40 8.80 7.00e-01 2.04e+00 1.58e+02 angle pdb=" N1 U C 24 " pdb=" C2 U C 24 " pdb=" O2 U C 24 " ideal model delta sigma weight residual 122.80 129.59 -6.79 7.00e-01 2.04e+00 9.40e+01 angle pdb=" O2 U C 90 " pdb=" C2 U C 90 " pdb=" N3 U C 90 " ideal model delta sigma weight residual 122.20 115.83 6.37 7.00e-01 2.04e+00 8.27e+01 angle pdb=" C1' U C 24 " pdb=" N1 U C 24 " pdb=" C2 U C 24 " ideal model delta sigma weight residual 117.70 128.23 -10.53 1.20e+00 6.94e-01 7.71e+01 angle pdb=" N1 U C 90 " pdb=" C2 U C 90 " pdb=" O2 U C 90 " ideal model delta sigma weight residual 122.80 128.54 -5.74 7.00e-01 2.04e+00 6.72e+01 ... (remaining 19378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.40: 8317 32.40 - 64.79: 276 64.79 - 97.19: 27 97.19 - 129.58: 3 129.58 - 161.98: 4 Dihedral angle restraints: 8627 sinusoidal: 4368 harmonic: 4259 Sorted by residual: dihedral pdb=" O4' U C 24 " pdb=" C1' U C 24 " pdb=" N1 U C 24 " pdb=" C2 U C 24 " ideal model delta sinusoidal sigma weight residual -160.00 1.98 -161.98 1 1.50e+01 4.44e-03 8.32e+01 dihedral pdb=" O4' U C 90 " pdb=" C1' U C 90 " pdb=" N1 U C 90 " pdb=" C2 U C 90 " ideal model delta sinusoidal sigma weight residual -128.00 18.37 -146.37 1 1.70e+01 3.46e-03 6.09e+01 dihedral pdb=" CA LEU A 9 " pdb=" C LEU A 9 " pdb=" N ASP A 10 " pdb=" CA ASP A 10 " ideal model delta harmonic sigma weight residual 180.00 155.04 24.96 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 8624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1725 0.073 - 0.146: 451 0.146 - 0.218: 51 0.218 - 0.291: 7 0.291 - 0.364: 4 Chirality restraints: 2238 Sorted by residual: chirality pdb=" C3' G C 92 " pdb=" C4' G C 92 " pdb=" O3' G C 92 " pdb=" C2' G C 92 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C3' A C 28 " pdb=" C4' A C 28 " pdb=" O3' A C 28 " pdb=" C2' A C 28 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CG LEU A 419 " pdb=" CB LEU A 419 " pdb=" CD1 LEU A 419 " pdb=" CD2 LEU A 419 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 2235 not shown) Planarity restraints: 2145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 86 " -0.023 2.00e-02 2.50e+03 2.99e-02 1.56e+01 pdb=" CG PHE A 86 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 PHE A 86 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE A 86 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 86 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 86 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 86 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 38 " 0.021 2.00e-02 2.50e+03 1.98e-02 7.87e+00 pdb=" CG TYR B 38 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 38 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 38 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 38 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 38 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 38 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 38 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 450 " 0.035 2.00e-02 2.50e+03 1.89e-02 7.16e+00 pdb=" CG TYR A 450 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 450 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 450 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 450 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 450 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 450 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 450 " 0.016 2.00e-02 2.50e+03 ... (remaining 2142 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3185 2.79 - 3.32: 11560 3.32 - 3.84: 22725 3.84 - 4.37: 27802 4.37 - 4.90: 44890 Nonbonded interactions: 110162 Sorted by model distance: nonbonded pdb=" O LEU A 101 " pdb=" O2' A C 47 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR A 560 " pdb=" O ASP A 585 " model vdw 2.277 3.040 nonbonded pdb=" OD1 ASP A1267 " pdb=" OH TYR A1294 " model vdw 2.292 3.040 nonbonded pdb=" OE2 GLU A 762 " pdb=" OG SER A 960 " model vdw 2.294 3.040 nonbonded pdb=" O GLN A 817 " pdb=" OH TYR A 882 " model vdw 2.308 3.040 ... (remaining 110157 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 17.510 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 0.105 14043 Z= 0.581 Angle : 1.109 16.407 19383 Z= 0.791 Chirality : 0.064 0.364 2238 Planarity : 0.006 0.059 2145 Dihedral : 15.480 161.978 5869 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.16 % Allowed : 3.36 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.09 (0.17), residues: 1437 helix: -3.06 (0.13), residues: 720 sheet: -1.80 (0.38), residues: 133 loop : -2.23 (0.21), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG A 71 TYR 0.049 0.005 TYR B 38 PHE 0.066 0.005 PHE A 86 TRP 0.027 0.005 TRP A 476 HIS 0.016 0.003 HIS B 14 Details of bonding type rmsd/Z covalent geometry : bond 0.01027 / 0.58 (14043) covalent geometry : angle 1.10901 / 0.79 (19383) hydrogen bonds : bond 0.16111 / 10.08 ( 549) hydrogen bonds : angle 8.25927 / 5.71 ( 1572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 295 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8389 (mttt) cc_final: 0.7966 (mtmt) REVERT: A 224 ASN cc_start: 0.6807 (m-40) cc_final: 0.6490 (m110) REVERT: A 234 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7740 (tttm) REVERT: A 255 ASN cc_start: 0.7166 (m110) cc_final: 0.6965 (m110) REVERT: A 268 LYS cc_start: 0.7770 (tppp) cc_final: 0.7257 (tttt) REVERT: A 350 ILE cc_start: 0.8228 (mt) cc_final: 0.7970 (mm) REVERT: A 395 ARG cc_start: 0.7657 (ttp-170) cc_final: 0.7269 (ttp80) REVERT: A 406 ASP cc_start: 0.7592 (m-30) cc_final: 0.6975 (t0) REVERT: A 428 ASP cc_start: 0.7713 (m-30) cc_final: 0.7452 (t0) REVERT: A 556 ASN cc_start: 0.7374 (m-40) cc_final: 0.7154 (t0) REVERT: A 596 ASP cc_start: 0.7926 (m-30) cc_final: 0.7667 (m-30) REVERT: A 661 ARG cc_start: 0.7355 (ptp90) cc_final: 0.7123 (ptp-170) REVERT: A 694 MET cc_start: 0.7894 (mmm) cc_final: 0.6961 (mmt) REVERT: A 703 THR cc_start: 0.8828 (m) cc_final: 0.8556 (p) REVERT: A 1003 LYS cc_start: 0.8090 (mttt) cc_final: 0.7832 (mtmm) REVERT: A 1039 TYR cc_start: 0.8211 (m-80) cc_final: 0.7939 (m-80) REVERT: A 1059 LYS cc_start: 0.7710 (mttp) cc_final: 0.7271 (mttm) REVERT: A 1286 ASN cc_start: 0.7616 (m-40) cc_final: 0.7354 (m-40) REVERT: A 1300 LYS cc_start: 0.6638 (mmmm) cc_final: 0.6407 (mtpt) REVERT: A 1364 GLN cc_start: 0.7748 (mt0) cc_final: 0.7307 (tm130) outliers start: 2 outliers final: 0 residues processed: 296 average time/residue: 0.6009 time to fit residues: 192.4630 Evaluate side-chains 180 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN A 194 GLN A 240 ASN A 255 ASN A 277 ASN A 501 ASN A 511 HIS A 522 ASN A 612 ASN A 844 GLN A 920 GLN A1252 ASN ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS A1311 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.196409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.146484 restraints weight = 14585.121| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.43 r_work: 0.3174 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14043 Z= 0.148 Angle : 0.622 11.722 19383 Z= 0.342 Chirality : 0.043 0.439 2238 Planarity : 0.005 0.044 2145 Dihedral : 18.137 154.098 2968 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.64 % Allowed : 10.63 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.19), residues: 1437 helix: -1.26 (0.17), residues: 742 sheet: -1.53 (0.39), residues: 127 loop : -1.77 (0.22), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 70 TYR 0.020 0.002 TYR A 450 PHE 0.016 0.002 PHE A 86 TRP 0.008 0.001 TRP A 464 HIS 0.007 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (14043) covalent geometry : angle 0.62179 / 0.34 (19383) hydrogen bonds : bond 0.05611 / 3.83 ( 549) hydrogen bonds : angle 5.30092 / 3.60 ( 1572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: A 26 LYS cc_start: 0.8547 (mttt) cc_final: 0.8340 (mtpt) REVERT: A 211 ILE cc_start: 0.8831 (mt) cc_final: 0.8580 (mp) REVERT: A 224 ASN cc_start: 0.6734 (m-40) cc_final: 0.6424 (m110) REVERT: A 234 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7804 (tttt) REVERT: A 255 ASN cc_start: 0.7307 (m-40) cc_final: 0.7103 (m110) REVERT: A 268 LYS cc_start: 0.7674 (tppp) cc_final: 0.7301 (ttmm) REVERT: A 350 ILE cc_start: 0.8202 (mt) cc_final: 0.7976 (mm) REVERT: A 397 ASP cc_start: 0.6759 (t70) cc_final: 0.6237 (t0) REVERT: A 406 ASP cc_start: 0.8045 (m-30) cc_final: 0.7311 (t0) REVERT: A 428 ASP cc_start: 0.8088 (m-30) cc_final: 0.7567 (t0) REVERT: A 556 ASN cc_start: 0.7645 (m-40) cc_final: 0.7215 (t0) REVERT: A 596 ASP cc_start: 0.8001 (m-30) cc_final: 0.7720 (m-30) REVERT: A 613 GLU cc_start: 0.7835 (tp30) cc_final: 0.7490 (tp30) REVERT: A 627 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7575 (mp0) REVERT: A 694 MET cc_start: 0.8078 (mmm) cc_final: 0.7781 (mmp) REVERT: A 921 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6493 (mm) REVERT: A 952 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7115 (pt0) REVERT: A 1018 VAL cc_start: 0.7161 (t) cc_final: 0.6907 (t) REVERT: A 1039 TYR cc_start: 0.8163 (m-80) cc_final: 0.7829 (m-80) REVERT: A 1286 ASN cc_start: 0.7923 (m-40) cc_final: 0.7577 (m-40) REVERT: A 1300 LYS cc_start: 0.6628 (mmmm) cc_final: 0.6125 (mtpt) REVERT: A 1333 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6968 (ppp80) REVERT: A 1344 ASP cc_start: 0.7707 (p0) cc_final: 0.7496 (p0) REVERT: A 1364 GLN cc_start: 0.7963 (mt0) cc_final: 0.7244 (tm130) outliers start: 33 outliers final: 8 residues processed: 202 average time/residue: 0.5525 time to fit residues: 121.4583 Evaluate side-chains 167 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1284 ASP Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1333 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 10 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 49 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 HIS A 88 ASN A 240 ASN A 255 ASN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 GLN A1241 HIS A1297 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.197756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.162347 restraints weight = 14787.185| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.61 r_work: 0.3143 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14043 Z= 0.118 Angle : 0.541 10.152 19383 Z= 0.297 Chirality : 0.041 0.387 2238 Planarity : 0.004 0.038 2145 Dihedral : 17.935 153.405 2968 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.48 % Allowed : 12.23 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.20), residues: 1437 helix: -0.34 (0.19), residues: 737 sheet: -1.07 (0.41), residues: 124 loop : -1.49 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.015 0.001 TYR A 450 PHE 0.012 0.001 PHE A 86 TRP 0.006 0.001 TRP A 464 HIS 0.006 0.001 HIS A1297 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (14043) covalent geometry : angle 0.54091 / 0.30 (19383) hydrogen bonds : bond 0.04696 / 3.22 ( 549) hydrogen bonds : angle 4.79130 / 3.23 ( 1572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8035 (mp10) REVERT: B 44 GLU cc_start: 0.8225 (tt0) cc_final: 0.8004 (tm-30) REVERT: B 84 ASN cc_start: 0.8059 (m-40) cc_final: 0.7806 (m-40) REVERT: A 26 LYS cc_start: 0.8657 (mttt) cc_final: 0.8454 (mtmt) REVERT: A 202 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7968 (t0) REVERT: A 224 ASN cc_start: 0.6777 (m-40) cc_final: 0.6407 (m110) REVERT: A 234 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7768 (tttt) REVERT: A 255 ASN cc_start: 0.7229 (m110) cc_final: 0.7014 (m110) REVERT: A 268 LYS cc_start: 0.7737 (tppp) cc_final: 0.7467 (ttmm) REVERT: A 397 ASP cc_start: 0.7021 (t70) cc_final: 0.6508 (t0) REVERT: A 406 ASP cc_start: 0.8148 (m-30) cc_final: 0.7549 (t0) REVERT: A 428 ASP cc_start: 0.8202 (m-30) cc_final: 0.7669 (t0) REVERT: A 556 ASN cc_start: 0.7665 (m-40) cc_final: 0.7283 (t0) REVERT: A 596 ASP cc_start: 0.8006 (m-30) cc_final: 0.7778 (m-30) REVERT: A 613 GLU cc_start: 0.7840 (tp30) cc_final: 0.7452 (tp30) REVERT: A 627 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7719 (mp0) REVERT: A 694 MET cc_start: 0.8170 (mmm) cc_final: 0.7774 (mmp) REVERT: A 703 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8463 (p) REVERT: A 929 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8013 (ttpp) REVERT: A 952 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7198 (pt0) REVERT: A 1018 VAL cc_start: 0.7915 (t) cc_final: 0.7652 (t) REVERT: A 1039 TYR cc_start: 0.8184 (m-80) cc_final: 0.7805 (m-80) REVERT: A 1286 ASN cc_start: 0.7946 (m-40) cc_final: 0.7586 (m-40) REVERT: A 1300 LYS cc_start: 0.6473 (mmmm) cc_final: 0.5999 (mtpt) REVERT: A 1364 GLN cc_start: 0.8011 (mt0) cc_final: 0.7360 (tm130) outliers start: 31 outliers final: 7 residues processed: 193 average time/residue: 0.5585 time to fit residues: 118.7666 Evaluate side-chains 170 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 68 optimal weight: 0.0570 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 HIS A 277 ASN A 698 HIS A 844 GLN A1297 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.197309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146186 restraints weight = 14659.824| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.67 r_work: 0.3155 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14043 Z= 0.123 Angle : 0.528 9.746 19383 Z= 0.289 Chirality : 0.041 0.377 2238 Planarity : 0.004 0.038 2145 Dihedral : 17.796 154.316 2968 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.32 % Allowed : 13.03 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.21), residues: 1437 helix: 0.08 (0.19), residues: 736 sheet: -0.80 (0.42), residues: 126 loop : -1.37 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 661 TYR 0.024 0.001 TYR A 529 PHE 0.013 0.001 PHE A1327 TRP 0.005 0.001 TRP A 464 HIS 0.007 0.001 HIS A1297 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (14043) covalent geometry : angle 0.52833 / 0.29 (19383) hydrogen bonds : bond 0.04420 / 3.04 ( 549) hydrogen bonds : angle 4.60700 / 3.11 ( 1572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.8001 (mp10) REVERT: B 84 ASN cc_start: 0.7978 (m-40) cc_final: 0.7720 (m-40) REVERT: A 26 LYS cc_start: 0.8535 (mttt) cc_final: 0.8332 (mtmt) REVERT: A 202 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7928 (t0) REVERT: A 224 ASN cc_start: 0.6751 (m-40) cc_final: 0.6373 (m110) REVERT: A 234 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7774 (tttt) REVERT: A 255 ASN cc_start: 0.7239 (m110) cc_final: 0.7028 (m110) REVERT: A 341 GLN cc_start: 0.7346 (tp40) cc_final: 0.6958 (tm-30) REVERT: A 364 ASP cc_start: 0.7456 (m-30) cc_final: 0.7181 (m-30) REVERT: A 397 ASP cc_start: 0.6864 (t70) cc_final: 0.6323 (t0) REVERT: A 406 ASP cc_start: 0.8052 (m-30) cc_final: 0.7448 (t0) REVERT: A 428 ASP cc_start: 0.8188 (m-30) cc_final: 0.7706 (t0) REVERT: A 556 ASN cc_start: 0.7715 (m-40) cc_final: 0.7236 (t0) REVERT: A 596 ASP cc_start: 0.7955 (m-30) cc_final: 0.7703 (m-30) REVERT: A 613 GLU cc_start: 0.7847 (tp30) cc_final: 0.7534 (tp30) REVERT: A 661 ARG cc_start: 0.7941 (ptp90) cc_final: 0.7555 (ptp-170) REVERT: A 694 MET cc_start: 0.8118 (mmm) cc_final: 0.7631 (mmp) REVERT: A 703 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8406 (p) REVERT: A 847 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6631 (pt) REVERT: A 961 LYS cc_start: 0.7272 (mmtt) cc_final: 0.6702 (mmtt) REVERT: A 1015 VAL cc_start: 0.7819 (OUTLIER) cc_final: 0.7616 (t) REVERT: A 1039 TYR cc_start: 0.8049 (m-80) cc_final: 0.7559 (m-80) REVERT: A 1286 ASN cc_start: 0.7950 (m-40) cc_final: 0.7580 (m-40) REVERT: A 1300 LYS cc_start: 0.6417 (mmmm) cc_final: 0.5868 (mtpt) REVERT: A 1333 ARG cc_start: 0.7488 (mtm110) cc_final: 0.6850 (ppp80) REVERT: A 1364 GLN cc_start: 0.7945 (mt0) cc_final: 0.7465 (tm-30) outliers start: 29 outliers final: 9 residues processed: 183 average time/residue: 0.5500 time to fit residues: 110.1676 Evaluate side-chains 166 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1284 ASP Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 110 optimal weight: 0.0770 chunk 131 optimal weight: 20.0000 chunk 36 optimal weight: 0.0970 chunk 34 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 63 optimal weight: 0.0570 chunk 38 optimal weight: 3.9990 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 HIS A 277 ASN A 844 GLN A 985 HIS A1297 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.199419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.162280 restraints weight = 14741.641| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.73 r_work: 0.3174 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14043 Z= 0.102 Angle : 0.504 10.315 19383 Z= 0.275 Chirality : 0.040 0.356 2238 Planarity : 0.003 0.037 2145 Dihedral : 17.648 152.310 2968 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.48 % Allowed : 14.07 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.21), residues: 1437 helix: 0.43 (0.19), residues: 737 sheet: -0.61 (0.44), residues: 126 loop : -1.25 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 653 TYR 0.019 0.001 TYR A 529 PHE 0.010 0.001 PHE A 970 TRP 0.007 0.001 TRP A 464 HIS 0.008 0.001 HIS A1297 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (14043) covalent geometry : angle 0.50410 / 0.27 (19383) hydrogen bonds : bond 0.03875 / 2.66 ( 549) hydrogen bonds : angle 4.35042 / 2.94 ( 1572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7986 (mp10) REVERT: B 84 ASN cc_start: 0.8015 (m-40) cc_final: 0.7754 (m-40) REVERT: A 1 MET cc_start: 0.1667 (tpp) cc_final: 0.1254 (ttt) REVERT: A 224 ASN cc_start: 0.6899 (m-40) cc_final: 0.6543 (m110) REVERT: A 234 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7826 (tttt) REVERT: A 341 GLN cc_start: 0.7361 (tp40) cc_final: 0.6984 (tm-30) REVERT: A 364 ASP cc_start: 0.7494 (m-30) cc_final: 0.7220 (m-30) REVERT: A 374 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6639 (pttt) REVERT: A 397 ASP cc_start: 0.7097 (t70) cc_final: 0.6515 (t0) REVERT: A 406 ASP cc_start: 0.8076 (m-30) cc_final: 0.7563 (t0) REVERT: A 419 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8522 (tp) REVERT: A 428 ASP cc_start: 0.8205 (m-30) cc_final: 0.7726 (t0) REVERT: A 556 ASN cc_start: 0.7634 (m-40) cc_final: 0.7219 (t0) REVERT: A 596 ASP cc_start: 0.7924 (m-30) cc_final: 0.7652 (m-30) REVERT: A 613 GLU cc_start: 0.7887 (tp30) cc_final: 0.7518 (tp30) REVERT: A 631 MET cc_start: 0.8305 (tpt) cc_final: 0.8054 (tpt) REVERT: A 694 MET cc_start: 0.8231 (mmm) cc_final: 0.7835 (mmp) REVERT: A 703 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8420 (p) REVERT: A 847 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6865 (pt) REVERT: A 1039 TYR cc_start: 0.8119 (m-80) cc_final: 0.7629 (m-80) REVERT: A 1043 MET cc_start: 0.8424 (mmt) cc_final: 0.8144 (mmp) REVERT: A 1255 LYS cc_start: 0.7059 (mmmt) cc_final: 0.6747 (mtpp) REVERT: A 1300 LYS cc_start: 0.6453 (mmmm) cc_final: 0.5898 (mtpt) REVERT: A 1333 ARG cc_start: 0.7669 (mtm110) cc_final: 0.6909 (ppp80) REVERT: A 1364 GLN cc_start: 0.8032 (mt0) cc_final: 0.7588 (tm-30) outliers start: 31 outliers final: 10 residues processed: 181 average time/residue: 0.5562 time to fit residues: 110.7496 Evaluate side-chains 166 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 23 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 8 optimal weight: 0.0170 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.3620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 HIS A 240 ASN A 277 ASN A 844 GLN A 971 GLN A1297 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.195956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.155804 restraints weight = 14554.092| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.94 r_work: 0.3113 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14043 Z= 0.153 Angle : 0.540 9.794 19383 Z= 0.291 Chirality : 0.042 0.358 2238 Planarity : 0.004 0.039 2145 Dihedral : 17.577 156.364 2968 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.80 % Allowed : 14.47 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.22), residues: 1437 helix: 0.54 (0.19), residues: 739 sheet: -0.53 (0.45), residues: 126 loop : -1.19 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 661 TYR 0.026 0.001 TYR A 529 PHE 0.016 0.002 PHE A1327 TRP 0.004 0.001 TRP A 883 HIS 0.008 0.001 HIS A1297 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (14043) covalent geometry : angle 0.53988 / 0.29 (19383) hydrogen bonds : bond 0.04483 / 3.07 ( 549) hydrogen bonds : angle 4.34642 / 2.93 ( 1572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: B 84 ASN cc_start: 0.8001 (m-40) cc_final: 0.7733 (m-40) REVERT: A 4 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8383 (mptt) REVERT: A 224 ASN cc_start: 0.6880 (m-40) cc_final: 0.6516 (m110) REVERT: A 234 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7837 (tttt) REVERT: A 235 ASN cc_start: 0.7656 (t0) cc_final: 0.7269 (t0) REVERT: A 310 THR cc_start: 0.3707 (OUTLIER) cc_final: 0.2876 (p) REVERT: A 340 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6378 (mmp-170) REVERT: A 341 GLN cc_start: 0.7381 (tp40) cc_final: 0.7000 (tm-30) REVERT: A 364 ASP cc_start: 0.7578 (m-30) cc_final: 0.7245 (m-30) REVERT: A 397 ASP cc_start: 0.7168 (t70) cc_final: 0.6577 (t0) REVERT: A 406 ASP cc_start: 0.8166 (m-30) cc_final: 0.7619 (t0) REVERT: A 419 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8464 (tp) REVERT: A 428 ASP cc_start: 0.8254 (m-30) cc_final: 0.7753 (t0) REVERT: A 556 ASN cc_start: 0.7673 (m-40) cc_final: 0.7213 (t0) REVERT: A 596 ASP cc_start: 0.7953 (m-30) cc_final: 0.7658 (m-30) REVERT: A 613 GLU cc_start: 0.7866 (tp30) cc_final: 0.7442 (tp30) REVERT: A 694 MET cc_start: 0.8155 (mmm) cc_final: 0.7661 (mmp) REVERT: A 703 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8446 (p) REVERT: A 961 LYS cc_start: 0.7400 (mmtt) cc_final: 0.6824 (mmtt) REVERT: A 1039 TYR cc_start: 0.8095 (m-80) cc_final: 0.7588 (m-80) REVERT: A 1043 MET cc_start: 0.8414 (mmt) cc_final: 0.8098 (mmp) REVERT: A 1063 ILE cc_start: 0.8437 (mt) cc_final: 0.8157 (tt) REVERT: A 1300 LYS cc_start: 0.6352 (mmmm) cc_final: 0.5885 (mtpt) REVERT: A 1333 ARG cc_start: 0.7689 (mtm110) cc_final: 0.6947 (ppp80) REVERT: A 1364 GLN cc_start: 0.8023 (mt0) cc_final: 0.7571 (tm-30) outliers start: 35 outliers final: 12 residues processed: 180 average time/residue: 0.6134 time to fit residues: 120.7676 Evaluate side-chains 164 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 844 GLN Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 94 optimal weight: 0.0470 chunk 141 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 HIS A 277 ASN A 357 ASN A 844 GLN A1224 ASN A1297 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.195115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.153435 restraints weight = 14513.770| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.99 r_work: 0.3121 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14043 Z= 0.178 Angle : 0.571 10.265 19383 Z= 0.304 Chirality : 0.043 0.357 2238 Planarity : 0.004 0.040 2145 Dihedral : 17.540 156.270 2968 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.56 % Allowed : 15.35 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.22), residues: 1437 helix: 0.57 (0.19), residues: 739 sheet: -0.55 (0.45), residues: 126 loop : -1.15 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 661 TYR 0.020 0.002 TYR A 450 PHE 0.017 0.002 PHE A1327 TRP 0.005 0.001 TRP A 18 HIS 0.009 0.001 HIS A1297 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (14043) covalent geometry : angle 0.57065 / 0.30 (19383) hydrogen bonds : bond 0.04700 / 3.23 ( 549) hydrogen bonds : angle 4.36857 / 2.95 ( 1572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.8029 (mp10) REVERT: B 84 ASN cc_start: 0.7942 (m-40) cc_final: 0.7717 (m-40) REVERT: A 1 MET cc_start: 0.2276 (tpp) cc_final: 0.1154 (ttt) REVERT: A 4 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8417 (mptt) REVERT: A 224 ASN cc_start: 0.6942 (m-40) cc_final: 0.6578 (m110) REVERT: A 234 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7861 (tttt) REVERT: A 310 THR cc_start: 0.3714 (OUTLIER) cc_final: 0.2887 (p) REVERT: A 340 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6578 (mmp-170) REVERT: A 341 GLN cc_start: 0.7331 (tp40) cc_final: 0.6949 (tm-30) REVERT: A 374 LYS cc_start: 0.6986 (mppt) cc_final: 0.6633 (pttt) REVERT: A 397 ASP cc_start: 0.7170 (t70) cc_final: 0.6603 (t0) REVERT: A 406 ASP cc_start: 0.8203 (m-30) cc_final: 0.7671 (t0) REVERT: A 428 ASP cc_start: 0.8197 (m-30) cc_final: 0.7727 (t0) REVERT: A 556 ASN cc_start: 0.7664 (m-40) cc_final: 0.7219 (t0) REVERT: A 596 ASP cc_start: 0.7961 (m-30) cc_final: 0.7655 (m-30) REVERT: A 613 GLU cc_start: 0.7769 (tp30) cc_final: 0.7464 (tp30) REVERT: A 694 MET cc_start: 0.8163 (mmm) cc_final: 0.7722 (mmp) REVERT: A 703 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8494 (p) REVERT: A 929 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7942 (ttpp) REVERT: A 961 LYS cc_start: 0.7420 (mmtt) cc_final: 0.6848 (mmtt) REVERT: A 1039 TYR cc_start: 0.8086 (m-80) cc_final: 0.7569 (m-80) REVERT: A 1043 MET cc_start: 0.8432 (mmt) cc_final: 0.8096 (mmp) REVERT: A 1056 GLU cc_start: 0.7260 (mt-10) cc_final: 0.7019 (tp30) REVERT: A 1059 LYS cc_start: 0.7425 (mmtm) cc_final: 0.7155 (mptp) REVERT: A 1063 ILE cc_start: 0.8465 (mt) cc_final: 0.8172 (tt) REVERT: A 1300 LYS cc_start: 0.6397 (mmmm) cc_final: 0.5942 (mtpt) REVERT: A 1333 ARG cc_start: 0.7707 (mtm110) cc_final: 0.6981 (ppp80) REVERT: A 1344 ASP cc_start: 0.7599 (p0) cc_final: 0.7397 (p0) REVERT: A 1364 GLN cc_start: 0.7990 (mt0) cc_final: 0.7551 (tm-30) outliers start: 32 outliers final: 17 residues processed: 173 average time/residue: 0.6178 time to fit residues: 117.2657 Evaluate side-chains 170 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1284 ASP Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 59 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 108 optimal weight: 0.0970 chunk 89 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 118 optimal weight: 0.0270 chunk 53 optimal weight: 0.3980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 HIS A 277 ASN A 844 GLN A1224 ASN A1297 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.198698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.160222 restraints weight = 14510.038| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.85 r_work: 0.3140 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14043 Z= 0.104 Angle : 0.521 10.302 19383 Z= 0.282 Chirality : 0.040 0.330 2238 Planarity : 0.003 0.041 2145 Dihedral : 17.439 152.040 2968 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.00 % Allowed : 16.23 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.22), residues: 1437 helix: 0.83 (0.20), residues: 741 sheet: -0.55 (0.45), residues: 128 loop : -1.03 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 653 TYR 0.013 0.001 TYR A 529 PHE 0.010 0.001 PHE A 970 TRP 0.007 0.001 TRP A 464 HIS 0.009 0.001 HIS A1297 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (14043) covalent geometry : angle 0.52063 / 0.28 (19383) hydrogen bonds : bond 0.03823 / 2.62 ( 549) hydrogen bonds : angle 4.21603 / 2.85 ( 1572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 ASN cc_start: 0.7991 (m-40) cc_final: 0.7741 (m-40) REVERT: A 1 MET cc_start: 0.2545 (tpp) cc_final: 0.1427 (ttt) REVERT: A 4 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8424 (mptt) REVERT: A 224 ASN cc_start: 0.6931 (m-40) cc_final: 0.6570 (m110) REVERT: A 234 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7857 (tttt) REVERT: A 310 THR cc_start: 0.3490 (OUTLIER) cc_final: 0.2687 (p) REVERT: A 340 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6435 (mmp-170) REVERT: A 341 GLN cc_start: 0.7322 (tp40) cc_final: 0.6956 (tm-30) REVERT: A 364 ASP cc_start: 0.7565 (m-30) cc_final: 0.7231 (m-30) REVERT: A 374 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6595 (pttt) REVERT: A 397 ASP cc_start: 0.7297 (t70) cc_final: 0.6745 (t0) REVERT: A 406 ASP cc_start: 0.8171 (m-30) cc_final: 0.7656 (t0) REVERT: A 428 ASP cc_start: 0.8277 (m-30) cc_final: 0.7775 (t0) REVERT: A 556 ASN cc_start: 0.7628 (m-40) cc_final: 0.7229 (t0) REVERT: A 596 ASP cc_start: 0.7937 (m-30) cc_final: 0.7664 (m-30) REVERT: A 613 GLU cc_start: 0.7828 (tp30) cc_final: 0.7498 (tp30) REVERT: A 661 ARG cc_start: 0.8035 (ptp90) cc_final: 0.7648 (ptp-170) REVERT: A 694 MET cc_start: 0.8169 (mmm) cc_final: 0.7765 (mmp) REVERT: A 703 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8467 (p) REVERT: A 929 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7977 (ttpp) REVERT: A 961 LYS cc_start: 0.7434 (mmtt) cc_final: 0.6895 (mmtt) REVERT: A 1039 TYR cc_start: 0.8147 (m-80) cc_final: 0.7641 (m-80) REVERT: A 1043 MET cc_start: 0.8444 (mmt) cc_final: 0.8135 (mmp) REVERT: A 1059 LYS cc_start: 0.7569 (mmtm) cc_final: 0.7301 (mptp) REVERT: A 1063 ILE cc_start: 0.8370 (mt) cc_final: 0.8091 (tt) REVERT: A 1170 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7311 (mm-30) REVERT: A 1300 LYS cc_start: 0.6338 (mmmm) cc_final: 0.5876 (mtpt) REVERT: A 1333 ARG cc_start: 0.7609 (mtm110) cc_final: 0.6977 (ppp80) REVERT: A 1364 GLN cc_start: 0.8007 (mt0) cc_final: 0.7588 (tm-30) outliers start: 25 outliers final: 13 residues processed: 170 average time/residue: 0.6121 time to fit residues: 114.0280 Evaluate side-chains 169 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 844 GLN Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1284 ASP Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 100 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 HIS A 277 ASN ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.198126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.150508 restraints weight = 14636.164| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.56 r_work: 0.3151 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14043 Z= 0.116 Angle : 0.526 10.466 19383 Z= 0.284 Chirality : 0.041 0.318 2238 Planarity : 0.003 0.040 2145 Dihedral : 17.372 153.609 2968 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.00 % Allowed : 16.23 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.22), residues: 1437 helix: 0.91 (0.19), residues: 741 sheet: -0.68 (0.45), residues: 130 loop : -0.97 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 653 TYR 0.014 0.001 TYR A 450 PHE 0.013 0.001 PHE A1327 TRP 0.005 0.001 TRP A 883 HIS 0.007 0.001 HIS A1297 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (14043) covalent geometry : angle 0.52583 / 0.28 (19383) hydrogen bonds : bond 0.03921 / 2.68 ( 549) hydrogen bonds : angle 4.19145 / 2.83 ( 1572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 ASN cc_start: 0.7928 (m-40) cc_final: 0.7667 (m-40) REVERT: A 1 MET cc_start: 0.2469 (tpp) cc_final: 0.1403 (ttt) REVERT: A 4 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8362 (mptt) REVERT: A 202 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.8011 (t0) REVERT: A 224 ASN cc_start: 0.6838 (m-40) cc_final: 0.6467 (m110) REVERT: A 234 LYS cc_start: 0.8192 (ttpt) cc_final: 0.7847 (tttt) REVERT: A 310 THR cc_start: 0.3802 (OUTLIER) cc_final: 0.3002 (p) REVERT: A 340 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6368 (mmp-170) REVERT: A 341 GLN cc_start: 0.7295 (tp40) cc_final: 0.6912 (tm-30) REVERT: A 350 ILE cc_start: 0.7843 (mm) cc_final: 0.7472 (mt) REVERT: A 364 ASP cc_start: 0.7510 (m-30) cc_final: 0.7152 (m-30) REVERT: A 374 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.6548 (pttt) REVERT: A 397 ASP cc_start: 0.7208 (t70) cc_final: 0.6644 (t0) REVERT: A 406 ASP cc_start: 0.8187 (m-30) cc_final: 0.7634 (t0) REVERT: A 428 ASP cc_start: 0.8245 (m-30) cc_final: 0.7730 (t0) REVERT: A 556 ASN cc_start: 0.7680 (m-40) cc_final: 0.7215 (t0) REVERT: A 596 ASP cc_start: 0.7918 (m-30) cc_final: 0.7633 (m-30) REVERT: A 613 GLU cc_start: 0.7810 (tp30) cc_final: 0.7449 (tp30) REVERT: A 661 ARG cc_start: 0.8018 (ptp90) cc_final: 0.7636 (ptp-170) REVERT: A 694 MET cc_start: 0.8135 (mmm) cc_final: 0.7708 (mmp) REVERT: A 703 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8403 (p) REVERT: A 857 LEU cc_start: 0.8185 (tt) cc_final: 0.7212 (mt) REVERT: A 929 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7863 (ttpp) REVERT: A 961 LYS cc_start: 0.7276 (mmtt) cc_final: 0.6770 (mmtt) REVERT: A 1039 TYR cc_start: 0.8041 (m-80) cc_final: 0.7483 (m-80) REVERT: A 1043 MET cc_start: 0.8388 (mmt) cc_final: 0.8057 (mmp) REVERT: A 1059 LYS cc_start: 0.7564 (mmtm) cc_final: 0.7302 (mptp) REVERT: A 1063 ILE cc_start: 0.8315 (mt) cc_final: 0.8038 (tt) REVERT: A 1170 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7189 (mm-30) REVERT: A 1300 LYS cc_start: 0.6299 (mmmm) cc_final: 0.5850 (mtpt) REVERT: A 1333 ARG cc_start: 0.7567 (mtm110) cc_final: 0.6919 (ppp80) REVERT: A 1364 GLN cc_start: 0.7942 (mt0) cc_final: 0.7524 (tm-30) outliers start: 25 outliers final: 15 residues processed: 171 average time/residue: 0.6331 time to fit residues: 118.4688 Evaluate side-chains 170 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1284 ASP Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 96 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 HIS A 277 ASN A 817 GLN A 844 GLN A1224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.198365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.150692 restraints weight = 14526.627| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.30 r_work: 0.3162 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14043 Z= 0.116 Angle : 0.531 10.380 19383 Z= 0.286 Chirality : 0.040 0.288 2238 Planarity : 0.004 0.041 2145 Dihedral : 17.298 153.380 2968 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.08 % Allowed : 16.55 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.22), residues: 1437 helix: 0.97 (0.20), residues: 739 sheet: -0.71 (0.45), residues: 130 loop : -0.92 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 653 TYR 0.015 0.001 TYR A 450 PHE 0.012 0.001 PHE A1327 TRP 0.008 0.001 TRP A 883 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (14043) covalent geometry : angle 0.53113 / 0.29 (19383) hydrogen bonds : bond 0.03911 / 2.67 ( 549) hydrogen bonds : angle 4.19799 / 2.84 ( 1572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 ASN cc_start: 0.7914 (m-40) cc_final: 0.7675 (m-40) REVERT: A 1 MET cc_start: 0.2583 (tpp) cc_final: 0.1702 (ttt) REVERT: A 4 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8359 (mptt) REVERT: A 224 ASN cc_start: 0.6898 (m-40) cc_final: 0.6541 (m110) REVERT: A 234 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7873 (tttt) REVERT: A 310 THR cc_start: 0.3489 (OUTLIER) cc_final: 0.2763 (p) REVERT: A 340 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6314 (mmp-170) REVERT: A 350 ILE cc_start: 0.7829 (mm) cc_final: 0.7460 (mt) REVERT: A 364 ASP cc_start: 0.7443 (m-30) cc_final: 0.7090 (m-30) REVERT: A 374 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6555 (pttt) REVERT: A 397 ASP cc_start: 0.7204 (t70) cc_final: 0.6643 (t0) REVERT: A 406 ASP cc_start: 0.8157 (m-30) cc_final: 0.7610 (t0) REVERT: A 428 ASP cc_start: 0.8258 (m-30) cc_final: 0.7770 (t0) REVERT: A 556 ASN cc_start: 0.7646 (m-40) cc_final: 0.7208 (t0) REVERT: A 596 ASP cc_start: 0.7902 (m-30) cc_final: 0.7597 (m-30) REVERT: A 613 GLU cc_start: 0.7798 (tp30) cc_final: 0.7427 (tp30) REVERT: A 661 ARG cc_start: 0.8063 (ptp90) cc_final: 0.7665 (ptp-170) REVERT: A 694 MET cc_start: 0.8141 (mmm) cc_final: 0.7734 (mmp) REVERT: A 703 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8406 (p) REVERT: A 929 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7862 (ttpp) REVERT: A 961 LYS cc_start: 0.7389 (mmtt) cc_final: 0.6890 (mmtt) REVERT: A 1039 TYR cc_start: 0.8082 (m-80) cc_final: 0.7510 (m-80) REVERT: A 1043 MET cc_start: 0.8379 (mmt) cc_final: 0.8032 (mmp) REVERT: A 1059 LYS cc_start: 0.7624 (mmtm) cc_final: 0.7311 (mptp) REVERT: A 1300 LYS cc_start: 0.6259 (mmmm) cc_final: 0.5752 (mtpt) REVERT: A 1333 ARG cc_start: 0.7557 (mtm110) cc_final: 0.6930 (ppp80) REVERT: A 1364 GLN cc_start: 0.7908 (mt0) cc_final: 0.7533 (tm-30) outliers start: 26 outliers final: 17 residues processed: 167 average time/residue: 0.5961 time to fit residues: 109.5180 Evaluate side-chains 170 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 844 GLN Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1284 ASP Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 84 optimal weight: 5.9990 chunk 91 optimal weight: 0.0870 chunk 9 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 HIS A 277 ASN ** A 844 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 = 0.4175 r_free = 0.4175 target = 0.198392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.160765 restraints weight = 14647.858| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.71 r_work: 0.3160 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.257 14043 Z= 0.241 Angle : 0.968 59.199 19383 Z= 0.583 Chirality : 0.040 0.288 2238 Planarity : 0.004 0.040 2145 Dihedral : 17.298 153.376 2968 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.68 % Allowed : 16.87 % Favored : 81.45 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.22), residues: 1437 helix: 0.97 (0.20), residues: 739 sheet: -0.71 (0.45), residues: 130 loop : -0.91 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 653 TYR 0.014 0.001 TYR A 450 PHE 0.012 0.001 PHE A1327 TRP 0.007 0.001 TRP A 883 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.24 (14043) covalent geometry : angle 0.96813 / 0.58 (19383) hydrogen bonds : bond 0.03914 / 2.68 ( 549) hydrogen bonds : angle 4.19739 / 2.84 ( 1572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4126.30 seconds wall clock time: 71 minutes 5.30 seconds (4265.30 seconds total)