Starting phenix.real_space_refine on Fri Jul 3 12:17:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pfs_71612/07_2026/9pfs_71612.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pfs_71612/07_2026/9pfs_71612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pfs_71612/07_2026/9pfs_71612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pfs_71612/07_2026/9pfs_71612.map" model { file = "/net/cci-nas-00/data/ceres_data/9pfs_71612/07_2026/9pfs_71612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pfs_71612/07_2026/9pfs_71612.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 2 5.21 5 S 75 5.16 5 C 8709 2.51 5 N 2322 2.21 5 O 2606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13731 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1376, 11219 Classifications: {'peptide': 1376} Link IDs: {'PTRANS': 47, 'TRANS': 1328} Chain breaks: 5 Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "C" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 430 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "D" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 478 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain breaks: 1 Chain: "E" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 839 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 1 Chain: "P" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "T" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 223 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 1, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ZAN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.94, per 1000 atoms: 0.21 Number of scatterers: 13731 At special positions: 0 Unit cell: (98.394, 125.902, 104.742, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 75 16.00 P 17 15.00 Mg 2 11.99 O 2606 8.00 N 2322 7.00 C 8709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 757.0 milliseconds 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3178 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 9 sheets defined 63.5% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 removed outlier: 3.510A pdb=" N CYS A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 removed outlier: 4.299A pdb=" N LEU A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 98 through 132 removed outlier: 3.962A pdb=" N VAL A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 201 through 228 Processing helix chain 'A' and resid 265 through 296 removed outlier: 3.902A pdb=" N LEU A 295 " --> pdb=" O CYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 327 through 333 removed outlier: 4.226A pdb=" N ILE A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'A' and resid 351 through 379 removed outlier: 4.400A pdb=" N PHE A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.812A pdb=" N LEU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 423 through 426 Processing helix chain 'A' and resid 435 through 448 Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.722A pdb=" N VAL A 488 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 489 " --> pdb=" O ALA A 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 489' Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.611A pdb=" N ILE A 549 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TRP A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 596 through 604 Processing helix chain 'A' and resid 633 through 651 Processing helix chain 'A' and resid 652 through 655 Processing helix chain 'A' and resid 666 through 675 Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 716 through 725 removed outlier: 3.553A pdb=" N LEU A 720 " --> pdb=" O CYS A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 737 removed outlier: 3.541A pdb=" N LEU A 735 " --> pdb=" O SER A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 801 Processing helix chain 'A' and resid 832 through 852 Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 901 through 920 removed outlier: 3.847A pdb=" N GLU A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 939 Processing helix chain 'A' and resid 940 through 944 removed outlier: 3.755A pdb=" N HIS A 944 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 966 Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 982 through 986 Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1003 through 1020 removed outlier: 4.175A pdb=" N GLU A1007 " --> pdb=" O ASP A1003 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1043 Processing helix chain 'A' and resid 1052 through 1060 Processing helix chain 'A' and resid 1072 through 1087 removed outlier: 5.091A pdb=" N LEU A1079 " --> pdb=" O GLU A1075 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ALA A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1099 Processing helix chain 'A' and resid 1099 through 1111 removed outlier: 4.514A pdb=" N MET A1111 " --> pdb=" O LEU A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1130 through 1143 removed outlier: 3.659A pdb=" N ALA A1134 " --> pdb=" O PRO A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1153 removed outlier: 3.503A pdb=" N GLU A1152 " --> pdb=" O ASN A1149 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS A1153 " --> pdb=" O ILE A1150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1149 through 1153' Processing helix chain 'A' and resid 1159 through 1174 Processing helix chain 'A' and resid 1175 through 1180 Processing helix chain 'A' and resid 1198 through 1212 Processing helix chain 'A' and resid 1223 through 1227 Processing helix chain 'A' and resid 1277 through 1281 Processing helix chain 'A' and resid 1282 through 1299 Processing helix chain 'A' and resid 1304 through 1317 Processing helix chain 'A' and resid 1320 through 1325 Processing helix chain 'A' and resid 1326 through 1328 No H-bonds generated for 'chain 'A' and resid 1326 through 1328' Processing helix chain 'A' and resid 1354 through 1359 Processing helix chain 'A' and resid 1365 through 1367 No H-bonds generated for 'chain 'A' and resid 1365 through 1367' Processing helix chain 'A' and resid 1368 through 1377 removed outlier: 3.591A pdb=" N TYR A1376 " --> pdb=" O LEU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1404 Processing helix chain 'A' and resid 1432 through 1443 Processing helix chain 'A' and resid 1452 through 1460 removed outlier: 3.808A pdb=" N GLU A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A1460 " --> pdb=" O TYR A1456 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 156 Processing helix chain 'B' and resid 157 through 164 removed outlier: 3.811A pdb=" N ALA B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'C' and resid 129 through 156 Processing helix chain 'C' and resid 161 through 183 removed outlier: 3.891A pdb=" N GLY C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 removed outlier: 3.735A pdb=" N LEU D 135 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 200 removed outlier: 3.538A pdb=" N GLU D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 151 Processing helix chain 'E' and resid 174 through 183 Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 203 through 210 Processing helix chain 'E' and resid 217 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.173A pdb=" N LYS A 80 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N VAL A 263 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 253 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.597A pdb=" N VAL A 614 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 691 through 694 Processing sheet with id=AA6, first strand: chain 'A' and resid 812 through 815 removed outlier: 3.829A pdb=" N ILE A 698 " --> pdb=" O TYR A 861 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 873 through 875 removed outlier: 3.817A pdb=" N ILE A 873 " --> pdb=" O TYR A 880 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1228 through 1231 removed outlier: 3.514A pdb=" N ILE A1410 " --> pdb=" O ILE A1243 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A1243 " --> pdb=" O ILE A1410 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A1241 " --> pdb=" O LEU A1412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1271 through 1272 749 hydrogen bonds defined for protein. 2178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4148 1.34 - 1.46: 1938 1.46 - 1.57: 7752 1.57 - 1.69: 31 1.69 - 1.81: 127 Bond restraints: 13996 Sorted by residual: bond pdb=" O3B ZAN A2203 " pdb=" PG ZAN A2203 " ideal model delta sigma weight residual 1.740 1.611 0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" N3A ZAN A2203 " pdb=" PB ZAN A2203 " ideal model delta sigma weight residual 1.697 1.610 0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C4 ZAN A2203 " pdb=" C5 ZAN A2203 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" N3A ZAN A2203 " pdb=" PA ZAN A2203 " ideal model delta sigma weight residual 1.689 1.610 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C5 ZAN A2203 " pdb=" C6 ZAN A2203 " ideal model delta sigma weight residual 1.407 1.482 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 13991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 18780 2.54 - 5.08: 165 5.08 - 7.62: 24 7.62 - 10.16: 6 10.16 - 12.70: 1 Bond angle restraints: 18976 Sorted by residual: angle pdb=" PA ZAN A2203 " pdb=" N3A ZAN A2203 " pdb=" PB ZAN A2203 " ideal model delta sigma weight residual 133.19 120.49 12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C GLY A 810 " pdb=" N ASP A 811 " pdb=" CA ASP A 811 " ideal model delta sigma weight residual 124.82 131.69 -6.87 1.78e+00 3.16e-01 1.49e+01 angle pdb=" C ALA A 830 " pdb=" N GLN A 831 " pdb=" CA GLN A 831 " ideal model delta sigma weight residual 121.54 128.74 -7.20 1.91e+00 2.74e-01 1.42e+01 angle pdb=" N ASN A1149 " pdb=" CA ASN A1149 " pdb=" C ASN A1149 " ideal model delta sigma weight residual 114.09 108.83 5.26 1.55e+00 4.16e-01 1.15e+01 angle pdb=" CA MET A1396 " pdb=" CB MET A1396 " pdb=" CG MET A1396 " ideal model delta sigma weight residual 114.10 120.69 -6.59 2.00e+00 2.50e-01 1.09e+01 ... (remaining 18971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.01: 8101 25.01 - 50.01: 433 50.01 - 75.02: 55 75.02 - 100.03: 8 100.03 - 125.03: 2 Dihedral angle restraints: 8599 sinusoidal: 3706 harmonic: 4893 Sorted by residual: dihedral pdb=" N3A ZAN A2203 " pdb=" O3B ZAN A2203 " pdb=" PB ZAN A2203 " pdb=" PG ZAN A2203 " ideal model delta sinusoidal sigma weight residual 12.34 -112.69 125.03 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" CA GLU A 349 " pdb=" C GLU A 349 " pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" O2B ZAN A2203 " pdb=" O3B ZAN A2203 " pdb=" PB ZAN A2203 " pdb=" PG ZAN A2203 " ideal model delta sinusoidal sigma weight residual -100.77 1.62 -102.39 1 3.00e+01 1.11e-03 1.30e+01 ... (remaining 8596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1581 0.039 - 0.079: 479 0.079 - 0.118: 120 0.118 - 0.157: 25 0.157 - 0.196: 9 Chirality restraints: 2214 Sorted by residual: chirality pdb=" CA ASP A 811 " pdb=" N ASP A 811 " pdb=" C ASP A 811 " pdb=" CB ASP A 811 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA ASN A 812 " pdb=" N ASN A 812 " pdb=" C ASN A 812 " pdb=" CB ASN A 812 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" C2' ZAN A2203 " pdb=" C1' ZAN A2203 " pdb=" C3' ZAN A2203 " pdb=" O2' ZAN A2203 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 2211 not shown) Planarity restraints: 2330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A1041 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C THR A1041 " 0.038 2.00e-02 2.50e+03 pdb=" O THR A1041 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS A1042 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1219 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" C VAL A1219 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL A1219 " 0.014 2.00e-02 2.50e+03 pdb=" N THR A1220 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 737 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.63e+00 pdb=" N PRO A 738 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 738 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 738 " 0.027 5.00e-02 4.00e+02 ... (remaining 2327 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 61 2.42 - 3.04: 8129 3.04 - 3.66: 21896 3.66 - 4.28: 33479 4.28 - 4.90: 55849 Nonbonded interactions: 119414 Sorted by model distance: nonbonded pdb=" OD1 ASN A 812 " pdb="MG MG A2202 " model vdw 1.794 2.170 nonbonded pdb="MG MG A2201 " pdb=" N3A ZAN A2203 " model vdw 2.063 2.250 nonbonded pdb=" OD2 ASP A 811 " pdb="MG MG A2201 " model vdw 2.089 2.170 nonbonded pdb=" OD1 ASP A 811 " pdb="MG MG A2202 " model vdw 2.104 2.170 nonbonded pdb=" OD1 ASP A 700 " pdb="MG MG A2201 " model vdw 2.115 2.170 ... (remaining 119409 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 130 through 183) selection = (chain 'C' and resid 130 through 183) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.680 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 13996 Z= 0.167 Angle : 0.636 12.700 18976 Z= 0.333 Chirality : 0.042 0.196 2214 Planarity : 0.004 0.048 2330 Dihedral : 14.620 125.032 5421 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.21), residues: 1635 helix: 1.58 (0.17), residues: 961 sheet: -2.16 (0.51), residues: 88 loop : -0.81 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 114 TYR 0.019 0.001 TYR A 772 PHE 0.017 0.001 PHE A 25 TRP 0.021 0.001 TRP A 480 HIS 0.013 0.001 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (13996) covalent geometry : angle 0.63593 / 0.33 (18976) hydrogen bonds : bond 0.10465 / 6.75 ( 749) hydrogen bonds : angle 5.29118 / 3.79 ( 2178) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.364 Fit side-chains REVERT: A 558 MET cc_start: 0.8502 (mmp) cc_final: 0.8270 (mmp) REVERT: A 694 LYS cc_start: 0.7416 (mtmm) cc_final: 0.6948 (mtpp) REVERT: E 187 MET cc_start: 0.5893 (mmt) cc_final: 0.5664 (ptp) REVERT: E 193 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6876 (mm-30) REVERT: E 221 GLU cc_start: 0.7587 (tp30) cc_final: 0.7237 (mm-30) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.4698 time to fit residues: 142.9741 Evaluate side-chains 202 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.0060 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN A 243 GLN A 255 HIS A 381 HIS A 593 ASN A 632 GLN A 638 GLN A1022 HIS A1098 GLN A1215 ASN A1247 ASN A1288 GLN A1338 HIS A1387 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.140520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.114114 restraints weight = 15847.429| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.56 r_work: 0.3247 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13996 Z= 0.123 Angle : 0.507 7.032 18976 Z= 0.271 Chirality : 0.039 0.161 2214 Planarity : 0.004 0.042 2330 Dihedral : 9.943 114.142 2058 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.32 % Allowed : 9.95 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.21), residues: 1635 helix: 1.81 (0.16), residues: 968 sheet: -2.07 (0.54), residues: 77 loop : -0.65 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 627 TYR 0.017 0.001 TYR A 221 PHE 0.018 0.001 PHE A 592 TRP 0.017 0.001 TRP A 480 HIS 0.003 0.001 HIS A 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (13996) covalent geometry : angle 0.50659 / 0.27 (18976) hydrogen bonds : bond 0.03624 / 2.38 ( 749) hydrogen bonds : angle 4.50400 / 3.23 ( 2178) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.419 Fit side-chains REVERT: A 396 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.5988 (ttp-170) REVERT: A 483 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8297 (pp) REVERT: A 1191 ILE cc_start: 0.7550 (pt) cc_final: 0.7317 (mt) REVERT: A 1410 ILE cc_start: 0.8054 (pt) cc_final: 0.7589 (mt) REVERT: A 1422 MET cc_start: 0.7985 (ttp) cc_final: 0.7666 (ttm) REVERT: A 1426 ILE cc_start: 0.8214 (mm) cc_final: 0.7855 (tp) REVERT: E 187 MET cc_start: 0.6646 (mmt) cc_final: 0.5531 (ptp) REVERT: E 193 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6887 (mm-30) outliers start: 20 outliers final: 8 residues processed: 210 average time/residue: 0.4343 time to fit residues: 101.0664 Evaluate side-chains 199 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1441 GLN Chi-restraints excluded: chain E residue 154 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 46 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 45 optimal weight: 0.0070 chunk 42 optimal weight: 0.3980 chunk 84 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN A 593 ASN A 831 GLN A1215 ASN A1247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.140610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.113865 restraints weight = 15826.957| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.62 r_work: 0.3217 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13996 Z= 0.102 Angle : 0.455 6.038 18976 Z= 0.246 Chirality : 0.038 0.158 2214 Planarity : 0.003 0.042 2330 Dihedral : 9.744 116.415 2058 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.84 % Allowed : 11.40 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.21), residues: 1635 helix: 1.98 (0.16), residues: 969 sheet: -1.99 (0.53), residues: 77 loop : -0.58 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 511 TYR 0.014 0.001 TYR A 221 PHE 0.014 0.001 PHE A 25 TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (13996) covalent geometry : angle 0.45550 / 0.25 (18976) hydrogen bonds : bond 0.03377 / 2.22 ( 749) hydrogen bonds : angle 4.29296 / 3.07 ( 2178) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.398 Fit side-chains REVERT: A 396 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.5944 (ttp-170) REVERT: A 483 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8295 (pp) REVERT: A 1044 ILE cc_start: 0.8003 (tp) cc_final: 0.7769 (tp) REVERT: A 1159 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7466 (tm) REVERT: A 1191 ILE cc_start: 0.7505 (pt) cc_final: 0.7274 (mt) REVERT: A 1255 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: A 1410 ILE cc_start: 0.8128 (pt) cc_final: 0.7746 (mt) REVERT: A 1426 ILE cc_start: 0.8184 (mm) cc_final: 0.7839 (tp) REVERT: B 161 SER cc_start: 0.8670 (p) cc_final: 0.8461 (m) REVERT: C 160 THR cc_start: 0.3979 (OUTLIER) cc_final: 0.3667 (t) REVERT: D 148 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7368 (ttm) REVERT: E 161 SER cc_start: 0.8230 (OUTLIER) cc_final: 0.8010 (m) REVERT: E 187 MET cc_start: 0.6638 (mmt) cc_final: 0.5538 (ptp) REVERT: E 193 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6770 (mm-30) outliers start: 28 outliers final: 9 residues processed: 214 average time/residue: 0.4600 time to fit residues: 109.1513 Evaluate side-chains 211 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1430 ASP Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 30 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 593 ASN A 609 ASN A 831 GLN A1098 GLN A1247 ASN A1338 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110676 restraints weight = 15659.271| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.72 r_work: 0.3133 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13996 Z= 0.169 Angle : 0.525 6.161 18976 Z= 0.280 Chirality : 0.041 0.159 2214 Planarity : 0.004 0.044 2330 Dihedral : 9.906 120.192 2058 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.70 % Allowed : 12.06 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.21), residues: 1635 helix: 1.85 (0.17), residues: 972 sheet: -1.75 (0.55), residues: 77 loop : -0.52 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 747 TYR 0.018 0.002 TYR A 453 PHE 0.021 0.002 PHE A 424 TRP 0.019 0.002 TRP A 480 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (13996) covalent geometry : angle 0.52478 / 0.28 (18976) hydrogen bonds : bond 0.03860 / 2.55 ( 749) hydrogen bonds : angle 4.30092 / 3.08 ( 2178) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.384 Fit side-chains REVERT: A 441 ASP cc_start: 0.7731 (m-30) cc_final: 0.7519 (m-30) REVERT: A 483 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8352 (pp) REVERT: A 772 TYR cc_start: 0.8190 (m-80) cc_final: 0.7979 (m-80) REVERT: A 1159 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7607 (tm) REVERT: A 1191 ILE cc_start: 0.7584 (pt) cc_final: 0.7369 (mt) REVERT: A 1426 ILE cc_start: 0.8308 (mm) cc_final: 0.7973 (tp) REVERT: B 161 SER cc_start: 0.8892 (p) cc_final: 0.8643 (m) REVERT: C 160 THR cc_start: 0.4131 (OUTLIER) cc_final: 0.3787 (t) REVERT: D 148 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7632 (ttm) REVERT: E 161 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.8050 (m) REVERT: E 187 MET cc_start: 0.6687 (mmt) cc_final: 0.5637 (ptp) REVERT: E 193 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6983 (mm-30) outliers start: 41 outliers final: 18 residues processed: 217 average time/residue: 0.4433 time to fit residues: 107.2623 Evaluate side-chains 208 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1323 LYS Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 158 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 160 optimal weight: 0.0000 chunk 14 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 133 optimal weight: 0.0370 chunk 140 optimal weight: 0.9990 overall best weight: 0.5666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 593 ASN A 831 GLN A 970 ASN A1098 GLN A1247 ASN A1338 HIS D 150 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.139241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.112239 restraints weight = 15810.138| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.73 r_work: 0.3111 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13996 Z= 0.103 Angle : 0.457 6.718 18976 Z= 0.248 Chirality : 0.038 0.151 2214 Planarity : 0.003 0.039 2330 Dihedral : 9.790 123.694 2058 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.70 % Allowed : 13.57 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.21), residues: 1635 helix: 2.02 (0.17), residues: 962 sheet: -1.58 (0.55), residues: 85 loop : -0.48 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 627 TYR 0.015 0.001 TYR A 221 PHE 0.014 0.001 PHE A 25 TRP 0.012 0.001 TRP A 932 HIS 0.003 0.001 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (13996) covalent geometry : angle 0.45734 / 0.25 (18976) hydrogen bonds : bond 0.03396 / 2.23 ( 749) hydrogen bonds : angle 4.20093 / 3.00 ( 2178) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.661 Fit side-chains REVERT: A 413 ASP cc_start: 0.8669 (t0) cc_final: 0.8413 (t0) REVERT: A 483 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8146 (pp) REVERT: A 772 TYR cc_start: 0.8057 (m-80) cc_final: 0.7802 (m-80) REVERT: A 864 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7467 (ttp80) REVERT: A 1044 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7913 (tp) REVERT: A 1159 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7190 (tm) REVERT: A 1191 ILE cc_start: 0.7441 (pt) cc_final: 0.7220 (mt) REVERT: A 1255 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.6863 (mt-10) REVERT: A 1426 ILE cc_start: 0.8128 (mm) cc_final: 0.7791 (tp) REVERT: B 161 SER cc_start: 0.8720 (p) cc_final: 0.8495 (m) REVERT: C 160 THR cc_start: 0.4083 (OUTLIER) cc_final: 0.3771 (t) REVERT: D 148 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7467 (ttm) REVERT: E 161 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.8058 (m) REVERT: E 187 MET cc_start: 0.6666 (mmt) cc_final: 0.5512 (ptp) REVERT: E 193 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6643 (mm-30) outliers start: 41 outliers final: 20 residues processed: 223 average time/residue: 0.4430 time to fit residues: 110.1060 Evaluate side-chains 211 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1323 LYS Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 31 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN A 831 GLN A 970 ASN A1247 ASN A1338 HIS D 150 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.107001 restraints weight = 15792.354| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.71 r_work: 0.3057 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13996 Z= 0.189 Angle : 0.539 6.639 18976 Z= 0.286 Chirality : 0.041 0.168 2214 Planarity : 0.004 0.042 2330 Dihedral : 9.895 125.274 2058 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.75 % Allowed : 13.24 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.21), residues: 1635 helix: 1.86 (0.17), residues: 962 sheet: -1.71 (0.54), residues: 87 loop : -0.48 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 479 TYR 0.017 0.002 TYR A 221 PHE 0.021 0.002 PHE A 424 TRP 0.019 0.002 TRP A 480 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (13996) covalent geometry : angle 0.53866 / 0.29 (18976) hydrogen bonds : bond 0.03981 / 2.62 ( 749) hydrogen bonds : angle 4.29574 / 3.07 ( 2178) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 189 time to evaluate : 0.552 Fit side-chains REVERT: A 413 ASP cc_start: 0.8596 (t0) cc_final: 0.8375 (t0) REVERT: A 483 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8266 (pp) REVERT: A 511 ARG cc_start: 0.7641 (tpt-90) cc_final: 0.7170 (ttm110) REVERT: A 772 TYR cc_start: 0.8325 (m-80) cc_final: 0.8093 (m-80) REVERT: A 813 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8587 (mt0) REVERT: A 842 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7102 (mptt) REVERT: A 864 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7487 (ttp80) REVERT: A 1159 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7349 (tm) REVERT: A 1191 ILE cc_start: 0.7530 (pt) cc_final: 0.7323 (mt) REVERT: A 1255 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: A 1278 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.6815 (mtm180) REVERT: A 1426 ILE cc_start: 0.8287 (mm) cc_final: 0.8085 (tp) REVERT: B 161 SER cc_start: 0.8801 (p) cc_final: 0.8585 (m) REVERT: C 160 THR cc_start: 0.4168 (OUTLIER) cc_final: 0.3835 (t) REVERT: D 148 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7682 (ttm) REVERT: E 161 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.8090 (m) REVERT: E 174 ARG cc_start: 0.7451 (ttm110) cc_final: 0.7222 (ttp-170) REVERT: E 187 MET cc_start: 0.6737 (mmt) cc_final: 0.5624 (ptp) REVERT: E 193 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7059 (mm-30) outliers start: 57 outliers final: 26 residues processed: 222 average time/residue: 0.4567 time to fit residues: 112.7359 Evaluate side-chains 213 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 813 GLN Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1278 ARG Chi-restraints excluded: chain A residue 1323 LYS Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 92 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 141 optimal weight: 0.0470 chunk 45 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 ASN A 831 GLN A 970 ASN A1098 GLN A1247 ASN A1338 HIS D 150 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.135513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108126 restraints weight = 15796.802| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.78 r_work: 0.3105 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13996 Z= 0.109 Angle : 0.466 7.021 18976 Z= 0.251 Chirality : 0.038 0.155 2214 Planarity : 0.003 0.040 2330 Dihedral : 9.785 129.217 2058 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.90 % Allowed : 14.49 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.21), residues: 1635 helix: 1.95 (0.17), residues: 964 sheet: -1.57 (0.54), residues: 85 loop : -0.42 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 437 TYR 0.015 0.001 TYR A 221 PHE 0.014 0.001 PHE A 25 TRP 0.012 0.001 TRP A 932 HIS 0.004 0.001 HIS A 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (13996) covalent geometry : angle 0.46604 / 0.25 (18976) hydrogen bonds : bond 0.03461 / 2.28 ( 749) hydrogen bonds : angle 4.18891 / 2.99 ( 2178) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.339 Fit side-chains REVERT: A 257 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8010 (tt0) REVERT: A 483 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8304 (pp) REVERT: A 511 ARG cc_start: 0.7767 (tpt-90) cc_final: 0.7363 (ttm110) REVERT: A 567 GLU cc_start: 0.8312 (tp30) cc_final: 0.8098 (mm-30) REVERT: A 772 TYR cc_start: 0.8405 (m-80) cc_final: 0.8176 (m-80) REVERT: A 813 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8572 (mt0) REVERT: A 842 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7299 (mptt) REVERT: A 864 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7654 (ttp80) REVERT: A 1159 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7552 (tm) REVERT: A 1191 ILE cc_start: 0.7570 (pt) cc_final: 0.7326 (mt) REVERT: A 1255 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7157 (mt-10) REVERT: A 1278 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.6922 (mtm180) REVERT: A 1408 ASN cc_start: 0.7921 (m-40) cc_final: 0.7471 (m-40) REVERT: A 1426 ILE cc_start: 0.8309 (mm) cc_final: 0.7986 (tp) REVERT: B 161 SER cc_start: 0.8922 (p) cc_final: 0.8630 (m) REVERT: C 160 THR cc_start: 0.4179 (OUTLIER) cc_final: 0.3837 (t) REVERT: D 148 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7633 (ttm) REVERT: E 161 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.8088 (m) REVERT: E 174 ARG cc_start: 0.7535 (ttm110) cc_final: 0.7305 (ttp-170) REVERT: E 187 MET cc_start: 0.6732 (mmt) cc_final: 0.5647 (ptp) REVERT: E 193 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7118 (mm-30) outliers start: 44 outliers final: 21 residues processed: 215 average time/residue: 0.4527 time to fit residues: 107.9948 Evaluate side-chains 206 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 813 GLN Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1278 ARG Chi-restraints excluded: chain A residue 1323 LYS Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 92 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 ASN A 831 GLN A1098 GLN A1247 ASN A1338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.134223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.106862 restraints weight = 15800.396| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.77 r_work: 0.3070 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13996 Z= 0.143 Angle : 0.499 7.968 18976 Z= 0.266 Chirality : 0.039 0.156 2214 Planarity : 0.003 0.040 2330 Dihedral : 9.776 130.099 2058 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.10 % Allowed : 14.76 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.21), residues: 1635 helix: 1.97 (0.17), residues: 959 sheet: -1.66 (0.52), residues: 87 loop : -0.45 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.016 0.001 TYR A 221 PHE 0.015 0.001 PHE A 424 TRP 0.013 0.001 TRP A 480 HIS 0.006 0.001 HIS A 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (13996) covalent geometry : angle 0.49893 / 0.27 (18976) hydrogen bonds : bond 0.03620 / 2.39 ( 749) hydrogen bonds : angle 4.19910 / 3.00 ( 2178) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.539 Fit side-chains REVERT: A 257 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7977 (tt0) REVERT: A 483 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8289 (pp) REVERT: A 511 ARG cc_start: 0.7770 (tpt-90) cc_final: 0.7334 (ttm110) REVERT: A 813 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8612 (mt0) REVERT: A 842 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7226 (mptt) REVERT: A 864 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7555 (ttp80) REVERT: A 1159 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7575 (tm) REVERT: A 1191 ILE cc_start: 0.7561 (pt) cc_final: 0.7326 (mt) REVERT: A 1255 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7190 (mt-10) REVERT: A 1278 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.6915 (mtm180) REVERT: A 1408 ASN cc_start: 0.7912 (m-40) cc_final: 0.7438 (m-40) REVERT: A 1426 ILE cc_start: 0.8353 (mm) cc_final: 0.8056 (tp) REVERT: B 161 SER cc_start: 0.8931 (p) cc_final: 0.8621 (m) REVERT: C 160 THR cc_start: 0.3932 (OUTLIER) cc_final: 0.3619 (t) REVERT: C 177 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6083 (mtt) REVERT: E 161 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.8095 (m) REVERT: E 174 ARG cc_start: 0.7537 (ttm110) cc_final: 0.7322 (ttp-170) REVERT: E 187 MET cc_start: 0.6733 (mmt) cc_final: 0.5637 (ptp) REVERT: E 193 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7118 (mm-30) outliers start: 47 outliers final: 25 residues processed: 207 average time/residue: 0.4568 time to fit residues: 105.6956 Evaluate side-chains 208 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 813 GLN Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1278 ARG Chi-restraints excluded: chain A residue 1323 LYS Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 0.0370 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 ASN A1098 GLN A1247 ASN A1338 HIS D 150 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.135341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.108432 restraints weight = 15732.669| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.72 r_work: 0.3066 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13996 Z= 0.129 Angle : 0.486 6.948 18976 Z= 0.260 Chirality : 0.039 0.152 2214 Planarity : 0.003 0.040 2330 Dihedral : 9.747 132.901 2058 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.96 % Allowed : 15.28 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.21), residues: 1635 helix: 1.98 (0.17), residues: 959 sheet: -1.65 (0.52), residues: 87 loop : -0.43 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.016 0.001 TYR A 221 PHE 0.014 0.001 PHE A 424 TRP 0.012 0.001 TRP A 932 HIS 0.004 0.001 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (13996) covalent geometry : angle 0.48612 / 0.26 (18976) hydrogen bonds : bond 0.03553 / 2.34 ( 749) hydrogen bonds : angle 4.18410 / 2.99 ( 2178) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 0.537 Fit side-chains REVERT: A 257 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7847 (tt0) REVERT: A 483 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8172 (pp) REVERT: A 511 ARG cc_start: 0.7547 (tpt-90) cc_final: 0.7054 (ttm110) REVERT: A 567 GLU cc_start: 0.8252 (tp30) cc_final: 0.8033 (mm-30) REVERT: A 813 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8579 (mt0) REVERT: A 842 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7015 (mptt) REVERT: A 864 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7489 (ttp80) REVERT: A 1159 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7340 (tm) REVERT: A 1191 ILE cc_start: 0.7457 (pt) cc_final: 0.7249 (mt) REVERT: A 1255 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: A 1278 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.6749 (mtm180) REVERT: A 1426 ILE cc_start: 0.8272 (mm) cc_final: 0.7972 (tp) REVERT: B 161 SER cc_start: 0.8853 (p) cc_final: 0.8545 (m) REVERT: C 160 THR cc_start: 0.3928 (OUTLIER) cc_final: 0.3623 (t) REVERT: C 177 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.5953 (mtt) REVERT: D 148 MET cc_start: 0.8008 (tpp) cc_final: 0.7670 (ttm) REVERT: E 174 ARG cc_start: 0.7408 (ttm110) cc_final: 0.7180 (ttp-170) REVERT: E 187 MET cc_start: 0.6686 (mmt) cc_final: 0.5544 (ptp) REVERT: E 193 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6930 (mm-30) outliers start: 45 outliers final: 25 residues processed: 210 average time/residue: 0.4250 time to fit residues: 99.0885 Evaluate side-chains 209 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 813 GLN Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1278 ARG Chi-restraints excluded: chain A residue 1323 LYS Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 ASN A 831 GLN A1098 GLN A1247 ASN A1288 GLN A1338 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.133288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.106410 restraints weight = 15738.047| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.59 r_work: 0.3120 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13996 Z= 0.125 Angle : 0.488 8.302 18976 Z= 0.264 Chirality : 0.038 0.151 2214 Planarity : 0.003 0.039 2330 Dihedral : 9.718 134.747 2058 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.83 % Allowed : 15.74 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.21), residues: 1635 helix: 2.01 (0.16), residues: 959 sheet: -1.64 (0.51), residues: 87 loop : -0.42 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.016 0.001 TYR A 221 PHE 0.013 0.001 PHE A 25 TRP 0.012 0.001 TRP A 480 HIS 0.004 0.001 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (13996) covalent geometry : angle 0.48801 / 0.26 (18976) hydrogen bonds : bond 0.03511 / 2.31 ( 749) hydrogen bonds : angle 4.17813 / 2.98 ( 2178) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 0.347 Fit side-chains REVERT: A 257 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7938 (tt0) REVERT: A 483 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8214 (pp) REVERT: A 511 ARG cc_start: 0.7607 (tpt-90) cc_final: 0.7167 (ttm110) REVERT: A 567 GLU cc_start: 0.8222 (tp30) cc_final: 0.8016 (mm-30) REVERT: A 842 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7152 (mptt) REVERT: A 1159 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7483 (tm) REVERT: A 1259 THR cc_start: 0.7944 (m) cc_final: 0.7689 (p) REVERT: A 1278 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.6831 (mtm180) REVERT: A 1408 ASN cc_start: 0.7875 (m-40) cc_final: 0.7437 (m-40) REVERT: B 161 SER cc_start: 0.8914 (p) cc_final: 0.8578 (m) REVERT: C 160 THR cc_start: 0.4038 (OUTLIER) cc_final: 0.3736 (t) REVERT: C 177 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.6059 (mtt) REVERT: D 148 MET cc_start: 0.8089 (tpp) cc_final: 0.7733 (ttm) REVERT: E 174 ARG cc_start: 0.7450 (ttm110) cc_final: 0.7218 (ttp-170) REVERT: E 187 MET cc_start: 0.6675 (mmt) cc_final: 0.5562 (ptp) REVERT: E 193 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6939 (mm-30) outliers start: 43 outliers final: 26 residues processed: 208 average time/residue: 0.4468 time to fit residues: 103.2990 Evaluate side-chains 208 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1278 ARG Chi-restraints excluded: chain A residue 1323 LYS Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 91 optimal weight: 0.0870 chunk 107 optimal weight: 0.5980 chunk 14 optimal weight: 0.0170 chunk 102 optimal weight: 1.9990 chunk 8 optimal weight: 0.0050 chunk 55 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 overall best weight: 0.2810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 ASN A 831 GLN A1098 GLN A1247 ASN A1288 GLN A1338 HIS D 150 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.137650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.110807 restraints weight = 15803.067| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.65 r_work: 0.3178 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13996 Z= 0.098 Angle : 0.460 6.984 18976 Z= 0.249 Chirality : 0.037 0.149 2214 Planarity : 0.003 0.040 2330 Dihedral : 9.593 139.173 2058 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.04 % Allowed : 16.53 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.21), residues: 1635 helix: 2.09 (0.16), residues: 970 sheet: -1.50 (0.52), residues: 85 loop : -0.39 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 479 TYR 0.014 0.001 TYR A 221 PHE 0.014 0.001 PHE A 25 TRP 0.011 0.001 TRP A 932 HIS 0.004 0.001 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (13996) covalent geometry : angle 0.46004 / 0.25 (18976) hydrogen bonds : bond 0.03220 / 2.11 ( 749) hydrogen bonds : angle 4.09089 / 2.92 ( 2178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4011.42 seconds wall clock time: 69 minutes 13.29 seconds (4153.29 seconds total)