Starting phenix.real_space_refine on Thu Jul 31 15:04:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ye6_39190/07_2025/8ye6_39190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ye6_39190/07_2025/8ye6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ye6_39190/07_2025/8ye6_39190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ye6_39190/07_2025/8ye6_39190.map" model { file = "/net/cci-nas-00/data/ceres_data/8ye6_39190/07_2025/8ye6_39190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ye6_39190/07_2025/8ye6_39190.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.135 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 4, 'GLU:plan': 13, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3} 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: 8.74, per 1000 atoms: 0.64 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: 3.45 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 5.35 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: 5.87 Time building geometry restraints manager: 4.16 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=" CB GLN A 83 " pdb=" CG GLN A 83 " ideal model delta sigma weight residual 1.520 1.438 0.082 3.00e-02 1.11e+03 7.45e+00 bond pdb=" CD LYS A1124 " pdb=" CE LYS A1124 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.78e+00 bond pdb=" CG ARG A 74 " pdb=" CD ARG A 74 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.76e+00 bond pdb=" CZ ARG A 78 " pdb=" NH2 ARG A 78 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.32e+00 bond pdb=" CB GLU A 84 " pdb=" CG GLU A 84 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.24e+00 ... (remaining 14038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 19024 3.28 - 6.56: 321 6.56 - 9.84: 33 9.84 - 13.13: 4 13.13 - 16.41: 1 Bond angle restraints: 19383 Sorted by residual: angle pdb=" CA LEU A 419 " pdb=" CB LEU A 419 " pdb=" CG LEU A 419 " ideal model delta sigma weight residual 116.30 132.71 -16.41 3.50e+00 8.16e-02 2.20e+01 angle pdb=" CA GLU A 102 " pdb=" CB GLU A 102 " pdb=" CG GLU A 102 " ideal model delta sigma weight residual 114.10 123.28 -9.18 2.00e+00 2.50e-01 2.11e+01 angle pdb=" C3' A C 28 " pdb=" O3' A C 28 " pdb=" P G C 29 " ideal model delta sigma weight residual 120.20 126.98 -6.78 1.50e+00 4.44e-01 2.04e+01 angle pdb=" CG ARG A 70 " pdb=" CD ARG A 70 " pdb=" NE ARG A 70 " ideal model delta sigma weight residual 112.00 121.86 -9.86 2.20e+00 2.07e-01 2.01e+01 angle pdb=" C3' A C 9 " pdb=" O3' A C 9 " pdb=" P A C 10 " ideal model delta sigma weight residual 120.20 126.92 -6.72 1.50e+00 4.44e-01 2.01e+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: 1818 0.073 - 0.146: 367 0.146 - 0.218: 42 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: 1.130 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 39.380 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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= 0.441 Angle : 1.070 16.407 19383 Z= 0.556 Chirality : 0.060 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.005 TRP A 476 HIS 0.016 0.003 HIS B 14 PHE 0.066 0.005 PHE A 86 TYR 0.049 0.005 TYR B 38 ARG 0.020 0.002 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.16111 ( 549) hydrogen bonds : angle 8.25927 ( 1572) covalent geometry : bond 0.01024 (14043) covalent geometry : angle 1.07046 (19383) *********************** 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 : 1.495 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: 0.6966 (m110) REVERT: A 268 LYS cc_start: 0.7770 (tppp) cc_final: 0.7256 (tttt) REVERT: A 350 ILE cc_start: 0.8228 (mt) cc_final: 0.7977 (mm) REVERT: A 395 ARG cc_start: 0.7657 (ttp-170) cc_final: 0.7270 (ttp80) REVERT: A 406 ASP cc_start: 0.7592 (m-30) cc_final: 0.6976 (t0) REVERT: A 428 ASP cc_start: 0.7713 (m-30) cc_final: 0.7451 (t0) REVERT: A 556 ASN cc_start: 0.7374 (m-40) cc_final: 0.7153 (t0) REVERT: A 596 ASP cc_start: 0.7926 (m-30) cc_final: 0.7668 (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: 0.6960 (mmt) REVERT: A 703 THR cc_start: 0.8828 (m) cc_final: 0.8555 (p) REVERT: A 1003 LYS cc_start: 0.8090 (mttt) cc_final: 0.7833 (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: 0.7311 (mttm) REVERT: A 1286 ASN cc_start: 0.7616 (m-40) cc_final: 0.7355 (m-40) REVERT: A 1300 LYS cc_start: 0.6638 (mmmm) cc_final: 0.6408 (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: 1.5053 time to fit residues: 480.0252 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 : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS A 194 GLN A 277 ASN A 501 ASN A 522 ASN A 698 HIS A 844 GLN A 863 ASN A 920 GLN A 971 GLN A1241 HIS ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS A1311 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.197836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.159668 restraints weight = 14566.280| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.75 r_work: 0.3144 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14043 Z= 0.134 Angle : 0.568 10.459 19383 Z= 0.305 Chirality : 0.040 0.242 2238 Planarity : 0.004 0.038 2145 Dihedral : 17.904 155.065 2968 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.64 % Allowed : 10.39 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.19), residues: 1437 helix: -0.97 (0.17), residues: 731 sheet: -1.08 (0.41), residues: 124 loop : -1.71 (0.22), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 464 HIS 0.006 0.001 HIS A 99 PHE 0.016 0.002 PHE A 86 TYR 0.017 0.001 TYR A 450 ARG 0.006 0.001 ARG A 655 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 549) hydrogen bonds : angle 4.92081 ( 1572) covalent geometry : bond 0.00274 (14043) covalent geometry : angle 0.56786 (19383) *********************** 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 231 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: A 4 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8426 (mmpt) REVERT: A 202 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.8042 (t0) REVERT: A 224 ASN cc_start: 0.6789 (m-40) cc_final: 0.6428 (m110) REVERT: A 234 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7829 (tttt) REVERT: A 255 ASN cc_start: 0.7230 (m110) cc_final: 0.7017 (m110) REVERT: A 268 LYS cc_start: 0.7820 (tppp) cc_final: 0.7475 (ttmm) REVERT: A 364 ASP cc_start: 0.7558 (m-30) cc_final: 0.7328 (m-30) REVERT: A 395 ARG cc_start: 0.7535 (ttp-170) cc_final: 0.7207 (ttp80) REVERT: A 406 ASP cc_start: 0.8172 (m-30) cc_final: 0.7568 (t0) REVERT: A 428 ASP cc_start: 0.8229 (m-30) cc_final: 0.7752 (t0) REVERT: A 502 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8452 (tt) REVERT: A 556 ASN cc_start: 0.7739 (m-40) cc_final: 0.7400 (t0) REVERT: A 596 ASP cc_start: 0.8036 (m-30) cc_final: 0.7809 (m-30) REVERT: A 599 LYS cc_start: 0.7653 (ttmp) cc_final: 0.6619 (ttpp) REVERT: A 613 GLU cc_start: 0.7944 (tp30) cc_final: 0.7677 (tp30) REVERT: A 661 ARG cc_start: 0.8048 (ptp90) cc_final: 0.7823 (ptp-170) REVERT: A 694 MET cc_start: 0.8196 (mmm) cc_final: 0.7833 (mmp) REVERT: A 952 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7305 (pt0) REVERT: A 1018 VAL cc_start: 0.7713 (t) cc_final: 0.7412 (t) REVERT: A 1039 TYR cc_start: 0.8192 (m-80) cc_final: 0.7803 (m-80) REVERT: A 1258 PHE cc_start: 0.7583 (t80) cc_final: 0.7271 (t80) REVERT: A 1286 ASN cc_start: 0.7913 (m-40) cc_final: 0.7572 (m-40) REVERT: A 1307 GLU cc_start: 0.7085 (tp30) cc_final: 0.6867 (tp30) REVERT: A 1364 GLN cc_start: 0.8062 (mt0) cc_final: 0.7362 (tm130) outliers start: 33 outliers final: 6 residues processed: 212 average time/residue: 1.2653 time to fit residues: 294.8716 Evaluate side-chains 161 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 502 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 65 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS A 88 ASN A 277 ASN A 511 HIS A 844 GLN A 971 GLN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1286 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.193539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141076 restraints weight = 14619.248| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.61 r_work: 0.3109 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14043 Z= 0.200 Angle : 0.608 11.715 19383 Z= 0.320 Chirality : 0.042 0.234 2238 Planarity : 0.004 0.040 2145 Dihedral : 17.760 156.718 2968 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.12 % Allowed : 12.71 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.21), residues: 1437 helix: -0.18 (0.19), residues: 737 sheet: -1.07 (0.42), residues: 126 loop : -1.47 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 18 HIS 0.007 0.001 HIS A 167 PHE 0.020 0.002 PHE A 86 TYR 0.026 0.002 TYR A 450 ARG 0.004 0.001 ARG A 461 Details of bonding type rmsd hydrogen bonds : bond 0.05275 ( 549) hydrogen bonds : angle 4.64213 ( 1572) covalent geometry : bond 0.00457 (14043) covalent geometry : angle 0.60823 (19383) *********************** 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 208 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: B 84 ASN cc_start: 0.7956 (m-40) cc_final: 0.7685 (m-40) REVERT: A 1 MET cc_start: 0.1642 (tpp) cc_final: 0.1282 (ttt) REVERT: A 4 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8307 (mmpt) REVERT: A 24 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6794 (tm-30) REVERT: A 224 ASN cc_start: 0.6762 (m-40) cc_final: 0.6403 (m110) REVERT: A 234 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7784 (tttt) REVERT: A 255 ASN cc_start: 0.7160 (m110) cc_final: 0.6933 (m110) REVERT: A 268 LYS cc_start: 0.7779 (tppp) cc_final: 0.7479 (ttmm) REVERT: A 349 GLU cc_start: 0.8240 (tp30) cc_final: 0.7586 (tp30) REVERT: A 397 ASP cc_start: 0.6929 (t70) cc_final: 0.6344 (t0) REVERT: A 406 ASP cc_start: 0.8163 (m-30) cc_final: 0.7584 (t0) REVERT: A 428 ASP cc_start: 0.8126 (m-30) cc_final: 0.7654 (t0) REVERT: A 556 ASN cc_start: 0.7700 (m-40) cc_final: 0.7324 (t0) REVERT: A 596 ASP cc_start: 0.7986 (m-30) cc_final: 0.7625 (m-30) REVERT: A 613 GLU cc_start: 0.7864 (tp30) cc_final: 0.7487 (tp30) REVERT: A 661 ARG cc_start: 0.8003 (ptp90) cc_final: 0.7747 (ptp-170) REVERT: A 694 MET cc_start: 0.8163 (mmm) cc_final: 0.7716 (mmp) REVERT: A 703 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8435 (p) REVERT: A 961 LYS cc_start: 0.7313 (mmtt) cc_final: 0.6705 (mmtt) REVERT: A 1039 TYR cc_start: 0.8107 (m-80) cc_final: 0.7671 (m-80) REVERT: A 1296 LYS cc_start: 0.7454 (mtmt) cc_final: 0.7132 (mtmt) REVERT: A 1307 GLU cc_start: 0.7053 (tp30) cc_final: 0.6824 (tp30) REVERT: A 1333 ARG cc_start: 0.7697 (mtm110) cc_final: 0.6878 (ppp80) REVERT: A 1364 GLN cc_start: 0.7934 (mt0) cc_final: 0.7517 (tm-30) outliers start: 39 outliers final: 12 residues processed: 192 average time/residue: 1.2958 time to fit residues: 272.2262 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 : 1.444 ------------------------------------------------------------------------------- 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 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 937 SER Chi-restraints excluded: chain A residue 1146 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 135 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 844 GLN ** A1252 ASN ** 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 = 0.4152 r_free = 0.4152 target = 0.195715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.157008 restraints weight = 14456.063| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.85 r_work: 0.3140 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14043 Z= 0.143 Angle : 0.540 10.080 19383 Z= 0.285 Chirality : 0.040 0.231 2238 Planarity : 0.003 0.040 2145 Dihedral : 17.507 155.347 2968 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.60 % Allowed : 13.27 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1437 helix: 0.30 (0.19), residues: 744 sheet: -0.74 (0.43), residues: 124 loop : -1.29 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.005 0.001 HIS A 99 PHE 0.017 0.002 PHE A1258 TYR 0.018 0.001 TYR A 450 ARG 0.005 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 549) hydrogen bonds : angle 4.33065 ( 1572) covalent geometry : bond 0.00320 (14043) covalent geometry : angle 0.53983 (19383) *********************** 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 211 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: B 55 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: B 84 ASN cc_start: 0.7976 (m-40) cc_final: 0.7709 (m-40) REVERT: A 4 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8423 (mmpt) REVERT: A 202 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.8059 (t0) REVERT: A 224 ASN cc_start: 0.6782 (m-40) cc_final: 0.6421 (m110) REVERT: A 234 LYS cc_start: 0.8218 (ttpt) cc_final: 0.7822 (tttt) REVERT: A 235 ASN cc_start: 0.7997 (t0) cc_final: 0.7541 (t0) REVERT: A 255 ASN cc_start: 0.7264 (m110) cc_final: 0.7023 (m110) REVERT: A 349 GLU cc_start: 0.8201 (tp30) cc_final: 0.7601 (tp30) REVERT: A 397 ASP cc_start: 0.7225 (t70) cc_final: 0.6682 (t0) REVERT: A 406 ASP cc_start: 0.8181 (m-30) cc_final: 0.7645 (t0) REVERT: A 428 ASP cc_start: 0.8132 (m-30) cc_final: 0.7715 (t0) REVERT: A 556 ASN cc_start: 0.7676 (m-40) cc_final: 0.7271 (t0) REVERT: A 596 ASP cc_start: 0.7910 (m-30) cc_final: 0.7665 (m-30) REVERT: A 613 GLU cc_start: 0.7960 (tp30) cc_final: 0.7597 (tp30) REVERT: A 661 ARG cc_start: 0.8076 (ptp90) cc_final: 0.7827 (ptp-170) REVERT: A 694 MET cc_start: 0.8166 (mmm) cc_final: 0.7769 (mmp) REVERT: A 703 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8469 (p) REVERT: A 811 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.6097 (tt) REVERT: A 844 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.7094 (mm-40) REVERT: A 929 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7960 (ttpp) REVERT: A 961 LYS cc_start: 0.7374 (mmtt) cc_final: 0.6797 (mmtt) REVERT: A 1015 VAL cc_start: 0.7969 (OUTLIER) cc_final: 0.7728 (t) REVERT: A 1039 TYR cc_start: 0.8159 (m-80) cc_final: 0.7643 (m-80) REVERT: A 1043 MET cc_start: 0.8418 (mmt) cc_final: 0.8110 (mmp) REVERT: A 1296 LYS cc_start: 0.7582 (mtmt) cc_final: 0.7238 (mtmt) REVERT: A 1297 HIS cc_start: 0.7186 (m170) cc_final: 0.6961 (m170) REVERT: A 1333 ARG cc_start: 0.7628 (mtm110) cc_final: 0.7027 (ppp80) REVERT: A 1364 GLN cc_start: 0.8021 (mt0) cc_final: 0.7632 (tm-30) outliers start: 45 outliers final: 15 residues processed: 192 average time/residue: 1.2338 time to fit residues: 260.1049 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 : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 390 LEU 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 811 LEU 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 957 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1284 ASP Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 0.0060 chunk 11 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 817 GLN A 985 HIS A1224 ASN A1256 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.196240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.163798 restraints weight = 14423.164| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.40 r_work: 0.3203 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14043 Z= 0.124 Angle : 0.523 9.268 19383 Z= 0.278 Chirality : 0.040 0.232 2238 Planarity : 0.003 0.049 2145 Dihedral : 17.395 154.231 2968 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.12 % Allowed : 14.63 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1437 helix: 0.65 (0.20), residues: 738 sheet: -0.36 (0.46), residues: 117 loop : -1.17 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 883 HIS 0.004 0.001 HIS A 99 PHE 0.015 0.001 PHE A1258 TYR 0.016 0.001 TYR A 450 ARG 0.009 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 549) hydrogen bonds : angle 4.19688 ( 1572) covalent geometry : bond 0.00273 (14043) covalent geometry : angle 0.52313 (19383) *********************** 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 193 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: B 84 ASN cc_start: 0.7930 (m-40) cc_final: 0.7676 (m-40) REVERT: A 4 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8380 (mmpt) REVERT: A 99 HIS cc_start: 0.7385 (m-70) cc_final: 0.7098 (m-70) REVERT: A 224 ASN cc_start: 0.6895 (m-40) cc_final: 0.6590 (m110) REVERT: A 234 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7869 (tttt) REVERT: A 364 ASP cc_start: 0.7493 (m-30) cc_final: 0.7133 (m-30) REVERT: A 397 ASP cc_start: 0.7147 (t70) cc_final: 0.6623 (t0) REVERT: A 406 ASP cc_start: 0.8039 (m-30) cc_final: 0.7549 (t0) REVERT: A 419 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8430 (tp) REVERT: A 428 ASP cc_start: 0.8079 (m-30) cc_final: 0.7679 (t0) REVERT: A 534 MET cc_start: 0.4891 (pp-130) cc_final: 0.4333 (ppp) REVERT: A 556 ASN cc_start: 0.7728 (m-40) cc_final: 0.7331 (t0) REVERT: A 596 ASP cc_start: 0.7862 (m-30) cc_final: 0.7592 (m-30) REVERT: A 613 GLU cc_start: 0.7823 (tp30) cc_final: 0.7478 (tp30) REVERT: A 661 ARG cc_start: 0.8007 (ptp90) cc_final: 0.7783 (ptp-170) REVERT: A 694 MET cc_start: 0.8088 (mmm) cc_final: 0.7695 (mmp) REVERT: A 703 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8475 (p) REVERT: A 811 LEU cc_start: 0.6333 (OUTLIER) cc_final: 0.6100 (tt) REVERT: A 942 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.6207 (mttp) REVERT: A 961 LYS cc_start: 0.7264 (mmtt) cc_final: 0.6778 (mmtt) REVERT: A 1015 VAL cc_start: 0.7923 (OUTLIER) cc_final: 0.7712 (t) REVERT: A 1039 TYR cc_start: 0.8152 (m-80) cc_final: 0.7651 (m-80) REVERT: A 1043 MET cc_start: 0.8405 (mmt) cc_final: 0.8085 (mmp) REVERT: A 1297 HIS cc_start: 0.7128 (m170) cc_final: 0.6878 (m170) REVERT: A 1333 ARG cc_start: 0.7527 (mtm110) cc_final: 0.7006 (ppp80) REVERT: A 1364 GLN cc_start: 0.7954 (mt0) cc_final: 0.7556 (tm-30) outliers start: 39 outliers final: 17 residues processed: 179 average time/residue: 1.2526 time to fit residues: 247.9222 Evaluate side-chains 171 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 390 LEU 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 696 LEU 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 811 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1146 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 277 ASN A 357 ASN A 844 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.196411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.163296 restraints weight = 14583.957| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.43 r_work: 0.3190 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14043 Z= 0.126 Angle : 0.517 9.275 19383 Z= 0.274 Chirality : 0.039 0.233 2238 Planarity : 0.003 0.052 2145 Dihedral : 17.276 154.020 2968 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.36 % Allowed : 14.95 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1437 helix: 0.89 (0.20), residues: 734 sheet: -0.32 (0.46), residues: 119 loop : -1.05 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 883 HIS 0.004 0.001 HIS A 99 PHE 0.013 0.001 PHE A1258 TYR 0.015 0.001 TYR A 450 ARG 0.010 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 549) hydrogen bonds : angle 4.09531 ( 1572) covalent geometry : bond 0.00281 (14043) covalent geometry : angle 0.51704 (19383) *********************** 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 197 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: B 41 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: B 84 ASN cc_start: 0.7911 (m-40) cc_final: 0.7684 (m-40) REVERT: A 4 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8530 (mptt) REVERT: A 43 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8032 (pt) REVERT: A 99 HIS cc_start: 0.7374 (m-70) cc_final: 0.6956 (m-70) REVERT: A 202 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8094 (t0) REVERT: A 224 ASN cc_start: 0.6875 (m-40) cc_final: 0.6558 (m110) REVERT: A 234 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7849 (tttt) REVERT: A 235 ASN cc_start: 0.7815 (t0) cc_final: 0.7404 (t0) REVERT: A 364 ASP cc_start: 0.7468 (m-30) cc_final: 0.7077 (m-30) REVERT: A 374 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6553 (pttt) REVERT: A 397 ASP cc_start: 0.6981 (t70) cc_final: 0.6498 (t0) REVERT: A 406 ASP cc_start: 0.8065 (m-30) cc_final: 0.7577 (t0) REVERT: A 419 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8435 (tp) REVERT: A 428 ASP cc_start: 0.8134 (m-30) cc_final: 0.7684 (t0) REVERT: A 556 ASN cc_start: 0.7706 (m-40) cc_final: 0.7324 (t0) REVERT: A 596 ASP cc_start: 0.7898 (m-30) cc_final: 0.7634 (m-30) REVERT: A 613 GLU cc_start: 0.7772 (tp30) cc_final: 0.7430 (tp30) REVERT: A 661 ARG cc_start: 0.8000 (ptp90) cc_final: 0.7776 (ptp-170) REVERT: A 694 MET cc_start: 0.8067 (mmm) cc_final: 0.7759 (mmp) REVERT: A 703 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8459 (p) REVERT: A 757 GLU cc_start: 0.8036 (tp30) cc_final: 0.7776 (mm-30) REVERT: A 811 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6100 (tt) REVERT: A 929 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7805 (ttpp) REVERT: A 942 LYS cc_start: 0.6418 (OUTLIER) cc_final: 0.6189 (mttp) REVERT: A 961 LYS cc_start: 0.7354 (mmtt) cc_final: 0.6801 (mmtt) REVERT: A 1015 VAL cc_start: 0.7867 (OUTLIER) cc_final: 0.7637 (t) REVERT: A 1043 MET cc_start: 0.8393 (mmt) cc_final: 0.8059 (mmp) REVERT: A 1056 GLU cc_start: 0.7276 (mt-10) cc_final: 0.7006 (tp30) REVERT: A 1297 HIS cc_start: 0.7015 (m170) cc_final: 0.6776 (m170) REVERT: A 1333 ARG cc_start: 0.7494 (mtm110) cc_final: 0.6988 (ppp80) REVERT: A 1364 GLN cc_start: 0.7932 (mt0) cc_final: 0.7614 (tm-30) outliers start: 42 outliers final: 18 residues processed: 182 average time/residue: 1.2406 time to fit residues: 247.9951 Evaluate side-chains 174 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 390 LEU 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 638 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 696 LEU 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 811 LEU Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1015 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 69 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 844 GLN A1224 ASN A1256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.194259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.162386 restraints weight = 14519.433| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.35 r_work: 0.3182 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14043 Z= 0.164 Angle : 0.554 10.152 19383 Z= 0.292 Chirality : 0.041 0.255 2238 Planarity : 0.004 0.062 2145 Dihedral : 17.212 154.935 2968 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.20 % Allowed : 15.27 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1437 helix: 0.87 (0.20), residues: 734 sheet: -0.51 (0.46), residues: 121 loop : -1.00 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 883 HIS 0.005 0.001 HIS A 167 PHE 0.015 0.002 PHE A1327 TYR 0.019 0.001 TYR A 450 ARG 0.012 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04541 ( 549) hydrogen bonds : angle 4.22149 ( 1572) covalent geometry : bond 0.00375 (14043) covalent geometry : angle 0.55392 (19383) *********************** 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 199 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: B 23 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7512 (mt0) REVERT: B 41 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7694 (tp30) REVERT: B 84 ASN cc_start: 0.7906 (m-40) cc_final: 0.7675 (m-40) REVERT: A 4 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8527 (mptt) REVERT: A 43 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8119 (pt) REVERT: A 99 HIS cc_start: 0.7364 (m-70) cc_final: 0.6870 (m-70) REVERT: A 202 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8082 (t0) REVERT: A 207 ASP cc_start: 0.7969 (t0) cc_final: 0.7658 (t0) REVERT: A 224 ASN cc_start: 0.6757 (m-40) cc_final: 0.6430 (m110) REVERT: A 234 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7862 (tttt) REVERT: A 235 ASN cc_start: 0.7872 (t0) cc_final: 0.7359 (t0) REVERT: A 310 THR cc_start: 0.3679 (OUTLIER) cc_final: 0.2880 (p) REVERT: A 350 ILE cc_start: 0.7908 (mm) cc_final: 0.7535 (mt) REVERT: A 397 ASP cc_start: 0.6908 (t70) cc_final: 0.6467 (t0) REVERT: A 406 ASP cc_start: 0.8050 (m-30) cc_final: 0.7590 (t0) REVERT: A 428 ASP cc_start: 0.8068 (m-30) cc_final: 0.7660 (t0) REVERT: A 556 ASN cc_start: 0.7796 (m-40) cc_final: 0.7413 (t0) REVERT: A 596 ASP cc_start: 0.7809 (m-30) cc_final: 0.7479 (m-30) REVERT: A 613 GLU cc_start: 0.7700 (tp30) cc_final: 0.7355 (tp30) REVERT: A 661 ARG cc_start: 0.7953 (ptp90) cc_final: 0.7702 (ptp-170) REVERT: A 694 MET cc_start: 0.8086 (mmm) cc_final: 0.7692 (mmp) REVERT: A 703 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8492 (p) REVERT: A 757 GLU cc_start: 0.8059 (tp30) cc_final: 0.7740 (tp30) REVERT: A 811 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6085 (tt) REVERT: A 919 ARG cc_start: 0.7785 (ttm170) cc_final: 0.7584 (ttt180) REVERT: A 929 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7831 (ttpp) REVERT: A 961 LYS cc_start: 0.7336 (mmtt) cc_final: 0.6846 (mmtt) REVERT: A 1015 VAL cc_start: 0.7827 (OUTLIER) cc_final: 0.7622 (t) REVERT: A 1039 TYR cc_start: 0.8088 (m-80) cc_final: 0.7609 (m-80) REVERT: A 1043 MET cc_start: 0.8438 (mmt) cc_final: 0.8067 (mmp) REVERT: A 1333 ARG cc_start: 0.7512 (mtm110) cc_final: 0.7052 (ppp80) REVERT: A 1364 GLN cc_start: 0.7883 (mt0) cc_final: 0.7583 (tm-30) outliers start: 40 outliers final: 21 residues processed: 183 average time/residue: 1.2437 time to fit residues: 250.4423 Evaluate side-chains 180 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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 41 GLU Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 43 ILE 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 345 GLU Chi-restraints excluded: chain A residue 390 LEU 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 696 LEU 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 811 LEU 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 957 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1146 VAL 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 55 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 124 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 844 GLN A1224 ASN A1256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.193914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.155539 restraints weight = 14424.142| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.81 r_work: 0.3125 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14043 Z= 0.176 Angle : 0.569 11.524 19383 Z= 0.299 Chirality : 0.041 0.281 2238 Planarity : 0.004 0.066 2145 Dihedral : 17.215 155.559 2968 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.04 % Allowed : 15.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1437 helix: 0.88 (0.20), residues: 734 sheet: -0.56 (0.46), residues: 121 loop : -1.00 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 883 HIS 0.005 0.001 HIS A 167 PHE 0.017 0.002 PHE A1327 TYR 0.019 0.001 TYR A 450 ARG 0.013 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04614 ( 549) hydrogen bonds : angle 4.22665 ( 1572) covalent geometry : bond 0.00407 (14043) covalent geometry : angle 0.56869 (19383) *********************** 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 186 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: B 23 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7550 (mt0) REVERT: B 41 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7828 (tp30) REVERT: B 84 ASN cc_start: 0.7947 (m-40) cc_final: 0.7703 (m-40) REVERT: A 4 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8518 (mptt) REVERT: A 43 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8189 (pt) REVERT: A 99 HIS cc_start: 0.7205 (m-70) cc_final: 0.6706 (m-70) REVERT: A 202 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8074 (t0) REVERT: A 224 ASN cc_start: 0.6860 (m-40) cc_final: 0.6536 (m110) REVERT: A 234 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7912 (tttt) REVERT: A 235 ASN cc_start: 0.7938 (t0) cc_final: 0.7456 (t0) REVERT: A 310 THR cc_start: 0.3941 (OUTLIER) cc_final: 0.3074 (p) REVERT: A 323 LYS cc_start: 0.8686 (mtpp) cc_final: 0.7987 (mptt) REVERT: A 338 LEU cc_start: 0.7518 (tp) cc_final: 0.7307 (tp) REVERT: A 350 ILE cc_start: 0.7922 (mm) cc_final: 0.7556 (mt) REVERT: A 374 LYS cc_start: 0.6885 (mppt) cc_final: 0.6598 (pttt) REVERT: A 397 ASP cc_start: 0.6961 (t70) cc_final: 0.6524 (t0) REVERT: A 406 ASP cc_start: 0.8133 (m-30) cc_final: 0.7640 (t0) REVERT: A 428 ASP cc_start: 0.8124 (m-30) cc_final: 0.7711 (t0) REVERT: A 534 MET cc_start: 0.4833 (pp-130) cc_final: 0.4462 (ppp) REVERT: A 556 ASN cc_start: 0.7850 (m-40) cc_final: 0.7452 (t0) REVERT: A 596 ASP cc_start: 0.7865 (m-30) cc_final: 0.7531 (m-30) REVERT: A 661 ARG cc_start: 0.8023 (ptp90) cc_final: 0.7778 (ptp-170) REVERT: A 694 MET cc_start: 0.8120 (mmm) cc_final: 0.7646 (mmp) REVERT: A 703 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8519 (p) REVERT: A 757 GLU cc_start: 0.8097 (tp30) cc_final: 0.7851 (tp30) REVERT: A 811 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.6122 (tt) REVERT: A 919 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7619 (ttt180) REVERT: A 929 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7872 (ttpp) REVERT: A 961 LYS cc_start: 0.7362 (mmtt) cc_final: 0.6867 (mmtt) REVERT: A 1015 VAL cc_start: 0.7873 (OUTLIER) cc_final: 0.7671 (t) REVERT: A 1039 TYR cc_start: 0.8094 (m-80) cc_final: 0.7588 (m-80) REVERT: A 1043 MET cc_start: 0.8453 (mmt) cc_final: 0.8086 (mmp) REVERT: A 1170 GLU cc_start: 0.8036 (pt0) cc_final: 0.7801 (pt0) REVERT: A 1252 ASN cc_start: 0.7111 (t0) cc_final: 0.6634 (p0) REVERT: A 1333 ARG cc_start: 0.7531 (mtm110) cc_final: 0.7078 (ppp80) REVERT: A 1364 GLN cc_start: 0.7915 (mt0) cc_final: 0.7554 (tm-30) outliers start: 38 outliers final: 20 residues processed: 175 average time/residue: 1.2405 time to fit residues: 238.8868 Evaluate side-chains 179 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 41 GLU Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 43 ILE 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 390 LEU 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 696 LEU 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 811 LEU 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 957 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 120 optimal weight: 0.1980 chunk 139 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 844 GLN A1224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.195623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.150604 restraints weight = 14354.740| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.05 r_work: 0.3158 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14043 Z= 0.133 Angle : 0.534 10.745 19383 Z= 0.283 Chirality : 0.040 0.293 2238 Planarity : 0.004 0.066 2145 Dihedral : 17.178 153.721 2968 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.20 % Allowed : 15.83 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1437 helix: 1.06 (0.20), residues: 734 sheet: -0.72 (0.44), residues: 130 loop : -0.90 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 464 HIS 0.005 0.001 HIS A1297 PHE 0.014 0.001 PHE A1258 TYR 0.014 0.001 TYR A 450 ARG 0.014 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 549) hydrogen bonds : angle 4.13594 ( 1572) covalent geometry : bond 0.00299 (14043) covalent geometry : angle 0.53360 (19383) *********************** 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 191 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 1.352 Fit side-chains revert: symmetry clash REVERT: B 23 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: B 41 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7796 (tp30) REVERT: B 84 ASN cc_start: 0.7917 (m-40) cc_final: 0.7688 (m-40) REVERT: A 4 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8579 (mptt) REVERT: A 43 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8146 (pt) REVERT: A 99 HIS cc_start: 0.7170 (m-70) cc_final: 0.6667 (m-70) REVERT: A 202 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8048 (t0) REVERT: A 224 ASN cc_start: 0.6826 (m-40) cc_final: 0.6499 (m110) REVERT: A 234 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7851 (tttt) REVERT: A 235 ASN cc_start: 0.7884 (t0) cc_final: 0.7421 (t0) REVERT: A 310 THR cc_start: 0.3617 (OUTLIER) cc_final: 0.2844 (p) REVERT: A 323 LYS cc_start: 0.8692 (mtpp) cc_final: 0.7999 (mptt) REVERT: A 338 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7278 (tp) REVERT: A 350 ILE cc_start: 0.7893 (mm) cc_final: 0.7525 (mt) REVERT: A 374 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6557 (pttt) REVERT: A 397 ASP cc_start: 0.6936 (t70) cc_final: 0.6498 (t0) REVERT: A 406 ASP cc_start: 0.8092 (m-30) cc_final: 0.7592 (t0) REVERT: A 428 ASP cc_start: 0.8121 (m-30) cc_final: 0.7786 (t0) REVERT: A 556 ASN cc_start: 0.7839 (m-40) cc_final: 0.7433 (t0) REVERT: A 596 ASP cc_start: 0.7862 (m-30) cc_final: 0.7583 (m-30) REVERT: A 613 GLU cc_start: 0.7700 (tp30) cc_final: 0.7434 (tp30) REVERT: A 694 MET cc_start: 0.8079 (mmm) cc_final: 0.7579 (mmp) REVERT: A 703 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8492 (p) REVERT: A 757 GLU cc_start: 0.8080 (tp30) cc_final: 0.7783 (tp30) REVERT: A 811 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.6122 (tt) REVERT: A 929 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7830 (ttpp) REVERT: A 961 LYS cc_start: 0.7375 (mmtt) cc_final: 0.6866 (mmtt) REVERT: A 1043 MET cc_start: 0.8437 (mmt) cc_final: 0.8107 (mmp) REVERT: A 1169 MET cc_start: 0.8755 (ttp) cc_final: 0.8495 (ttm) REVERT: A 1252 ASN cc_start: 0.7191 (t0) cc_final: 0.6643 (p0) REVERT: A 1333 ARG cc_start: 0.7503 (mtm110) cc_final: 0.7080 (ppp80) REVERT: A 1364 GLN cc_start: 0.7865 (mt0) cc_final: 0.7559 (tm-30) outliers start: 40 outliers final: 21 residues processed: 176 average time/residue: 1.2997 time to fit residues: 252.6692 Evaluate side-chains 178 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 41 GLU Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 43 ILE 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 338 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 390 LEU 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 696 LEU 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 811 LEU Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1284 ASP 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 120 optimal weight: 5.9990 chunk 104 optimal weight: 0.2980 chunk 80 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 77 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 124 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 844 GLN A1224 ASN A1256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.196182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.164411 restraints weight = 14404.628| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.25 r_work: 0.3217 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14043 Z= 0.126 Angle : 0.536 14.155 19383 Z= 0.282 Chirality : 0.040 0.292 2238 Planarity : 0.004 0.070 2145 Dihedral : 17.160 153.447 2968 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.88 % Allowed : 16.55 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1437 helix: 1.13 (0.20), residues: 734 sheet: -0.73 (0.44), residues: 130 loop : -0.89 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 464 HIS 0.006 0.001 HIS A1297 PHE 0.015 0.001 PHE A1258 TYR 0.014 0.001 TYR A 450 ARG 0.015 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 549) hydrogen bonds : angle 4.09948 ( 1572) covalent geometry : bond 0.00281 (14043) covalent geometry : angle 0.53648 (19383) ********************** 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 183 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: B 23 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7528 (mt0) REVERT: B 41 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7769 (tp30) REVERT: B 70 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8302 (mm) REVERT: B 84 ASN cc_start: 0.7905 (m-40) cc_final: 0.7668 (m-40) REVERT: A 4 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8570 (mptt) REVERT: A 43 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8112 (pt) REVERT: A 99 HIS cc_start: 0.7105 (m-70) cc_final: 0.6655 (m-70) REVERT: A 202 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8033 (t0) REVERT: A 224 ASN cc_start: 0.6846 (m-40) cc_final: 0.6529 (m110) REVERT: A 234 LYS cc_start: 0.8152 (ttpt) cc_final: 0.7851 (tttt) REVERT: A 235 ASN cc_start: 0.7898 (t0) cc_final: 0.7665 (t0) REVERT: A 310 THR cc_start: 0.3808 (OUTLIER) cc_final: 0.3075 (p) REVERT: A 323 LYS cc_start: 0.8652 (mtpp) cc_final: 0.7971 (mptt) REVERT: A 338 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7252 (tp) REVERT: A 350 ILE cc_start: 0.7884 (mm) cc_final: 0.7520 (mt) REVERT: A 374 LYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6573 (pttt) REVERT: A 397 ASP cc_start: 0.6678 (t70) cc_final: 0.6226 (t0) REVERT: A 406 ASP cc_start: 0.8028 (m-30) cc_final: 0.7567 (t0) REVERT: A 419 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8416 (tp) REVERT: A 428 ASP cc_start: 0.8035 (m-30) cc_final: 0.7790 (t0) REVERT: A 556 ASN cc_start: 0.7785 (m-40) cc_final: 0.7428 (t0) REVERT: A 596 ASP cc_start: 0.7874 (m-30) cc_final: 0.7605 (m-30) REVERT: A 613 GLU cc_start: 0.7661 (tp30) cc_final: 0.7389 (tp30) REVERT: A 694 MET cc_start: 0.8035 (mmm) cc_final: 0.7552 (mmp) REVERT: A 703 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8473 (p) REVERT: A 757 GLU cc_start: 0.7961 (tp30) cc_final: 0.7655 (tp30) REVERT: A 811 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.6118 (tt) REVERT: A 929 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7816 (ttpp) REVERT: A 961 LYS cc_start: 0.7367 (mmtt) cc_final: 0.6888 (mmtt) REVERT: A 1043 MET cc_start: 0.8444 (mmt) cc_final: 0.8118 (mmp) REVERT: A 1056 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6946 (tp30) REVERT: A 1169 MET cc_start: 0.8703 (ttp) cc_final: 0.8446 (ttm) REVERT: A 1252 ASN cc_start: 0.7237 (t0) cc_final: 0.6785 (p0) REVERT: A 1333 ARG cc_start: 0.7484 (mtm110) cc_final: 0.7079 (ppp80) REVERT: A 1364 GLN cc_start: 0.7791 (mt0) cc_final: 0.7548 (tm-30) outliers start: 36 outliers final: 20 residues processed: 169 average time/residue: 1.2402 time to fit residues: 229.9679 Evaluate side-chains 174 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain A residue 43 ILE 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 338 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 390 LEU 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 638 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 696 LEU 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 811 LEU 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 957 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1284 ASP 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 124 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.195368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.158241 restraints weight = 14396.476| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.60 r_work: 0.3182 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14043 Z= 0.150 Angle : 0.563 18.793 19383 Z= 0.293 Chirality : 0.040 0.291 2238 Planarity : 0.004 0.072 2145 Dihedral : 17.167 154.418 2968 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.72 % Allowed : 16.55 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1437 helix: 1.07 (0.20), residues: 740 sheet: -0.73 (0.44), residues: 130 loop : -0.91 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.005 0.001 HIS A1297 PHE 0.015 0.002 PHE A 539 TYR 0.017 0.001 TYR A 450 ARG 0.015 0.001 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 549) hydrogen bonds : angle 4.12400 ( 1572) covalent geometry : bond 0.00342 (14043) covalent geometry : angle 0.56345 (19383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9008.46 seconds wall clock time: 154 minutes 27.97 seconds (9267.97 seconds total)